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Conserved domains on  [gi|117647236|ref|NP_034288|]
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KH domain-containing, RNA-binding, signal transduction-associated protein 3 isoform 1 [Mus musculus]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
KH-I_KHDRBS3 cd22470
type I K homology (KH) RNA-binding domain found in KH domain-containing, RNA-binding, signal ...
 48-160 2.38e-70

type I K homology (KH) RNA-binding domain found in KH domain-containing, RNA-binding, signal transduction-associated protein 3 (KHDRBS3) and similar proteins; KHDRBS3, also called RNA-binding protein T-Star, or Sam68-like mammalian protein 2, or SLM-2, or Sam68-like phosphotyrosine protein, is an RNA-binding protein that plays a role in the regulation of alternative splicing and influences mRNA splice site selection and exon inclusion. It binds optimally to RNA containing 5'-[AU]UAA-3' as a bipartite motif spaced by more than 15 nucleotides. It also binds poly(A). KHDRBS3 may play a role as a negative regulator of cell growth.


:

Pssm-ID: 411898 [Multi-domain]  Cd Length: 113  Bit Score: 214.91  E-value: 2.38e-70
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117647236  48 VVINKNMKLGQKVLIPVKQFPKFNFVGKLLGPRGNSLKRLQEETLTKMSILGKGSMRDKAKEEELRKSGEAKYFHLNDDL 127
Cdd:cd22470    1 VVINKNMKLGQKVLIPVKQFPKFNFVGKLLGPRGNSLKRLQEETLTKMSILGKGSMRDKAKEEELRKSGEAKYFHLNDDL 80

                         90       100       110
                 ....*....|....*....|....*....|...
gi 117647236 128 HVLIEVFAPPAEAYARMGHALEEIKKFLIPDYN 160
Cdd:cd22470   81 HVLIEVFAPPAEAYARMGHALEEIKKFLIPDYN 113
Sam68-YY pfam16568
Tyrosine-rich domain of Sam68; Sam68-YY is a short tyrosine-rich domain on Src-associated in ...
 266-320 3.40e-28

Tyrosine-rich domain of Sam68; Sam68-YY is a short tyrosine-rich domain on Src-associated in mitosis, 68 kDa protein (Sam68), a protein that regulates TCF-1 alternative splicing. It is a crucial binding-partner of the APC-Arm domain that forms a superhelix with a positively charged groove, the surface-residues of which groove form numerous interactions with Sam68-YY to fix it in a bent conformation. APC-Arm is the armadillo repeat domain of the tumour-suppressor protein adenomatous polyposis coli or APC. APC plays plays important roles in Wnt signalling and other cellular processes.


:

Pssm-ID: 465182  Cd Length: 55  Bit Score: 104.07  E-value: 3.40e-28
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 117647236  266 YGEYDYDDGYGTAYDEQSYDSYDNSYSTPAQSAADYYDYGHGLSEDAYDSYGQEE 320
Cdd:pfam16568   1 YEEYGYDDGYGGEYDEQSYESYDNSYYSQAQSDPEYYDYGHGESQESYDSYGQEE 55
Qua1 pfam16274
Qua1 domain; This domain, approximately 40 residues in length, is mainly found in KH-domain ...
 4-53 2.69e-25

Qua1 domain; This domain, approximately 40 residues in length, is mainly found in KH-domain containing, RNA-binding, signal transduction-associated protein 1 from yeast to human. It forms a homodimer composed of a perpendicular interaction of two helical hairpins, and the Qua1 domain is sufficient for homodimerization which is required for the regulation of alternative splicing.


:

Pssm-ID: 465079  Cd Length: 52  Bit Score: 96.34  E-value: 2.69e-25
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 117647236    4 KYLPELMAEKDSLDPSFTHALRLVNREIEKFQKGEGK--EEEKYIDVVINKN 53
Cdd:pfam16274   1 KYLPELMAEKDSLDPSFTHAMQLLSAEIEKIQKGESKkdDEEKYLDLFSNKN 52
 
Name Accession Description Interval E-value
KH-I_KHDRBS3 cd22470
type I K homology (KH) RNA-binding domain found in KH domain-containing, RNA-binding, signal ...
 48-160 2.38e-70

type I K homology (KH) RNA-binding domain found in KH domain-containing, RNA-binding, signal transduction-associated protein 3 (KHDRBS3) and similar proteins; KHDRBS3, also called RNA-binding protein T-Star, or Sam68-like mammalian protein 2, or SLM-2, or Sam68-like phosphotyrosine protein, is an RNA-binding protein that plays a role in the regulation of alternative splicing and influences mRNA splice site selection and exon inclusion. It binds optimally to RNA containing 5'-[AU]UAA-3' as a bipartite motif spaced by more than 15 nucleotides. It also binds poly(A). KHDRBS3 may play a role as a negative regulator of cell growth.


Pssm-ID: 411898 [Multi-domain]  Cd Length: 113  Bit Score: 214.91  E-value: 2.38e-70
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117647236  48 VVINKNMKLGQKVLIPVKQFPKFNFVGKLLGPRGNSLKRLQEETLTKMSILGKGSMRDKAKEEELRKSGEAKYFHLNDDL 127
Cdd:cd22470    1 VVINKNMKLGQKVLIPVKQFPKFNFVGKLLGPRGNSLKRLQEETLTKMSILGKGSMRDKAKEEELRKSGEAKYFHLNDDL 80

                         90       100       110
                 ....*....|....*....|....*....|...
gi 117647236 128 HVLIEVFAPPAEAYARMGHALEEIKKFLIPDYN 160
Cdd:cd22470   81 HVLIEVFAPPAEAYARMGHALEEIKKFLIPDYN 113
Sam68-YY pfam16568
Tyrosine-rich domain of Sam68; Sam68-YY is a short tyrosine-rich domain on Src-associated in ...
 266-320 3.40e-28

Tyrosine-rich domain of Sam68; Sam68-YY is a short tyrosine-rich domain on Src-associated in mitosis, 68 kDa protein (Sam68), a protein that regulates TCF-1 alternative splicing. It is a crucial binding-partner of the APC-Arm domain that forms a superhelix with a positively charged groove, the surface-residues of which groove form numerous interactions with Sam68-YY to fix it in a bent conformation. APC-Arm is the armadillo repeat domain of the tumour-suppressor protein adenomatous polyposis coli or APC. APC plays plays important roles in Wnt signalling and other cellular processes.


Pssm-ID: 465182  Cd Length: 55  Bit Score: 104.07  E-value: 3.40e-28
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 117647236  266 YGEYDYDDGYGTAYDEQSYDSYDNSYSTPAQSAADYYDYGHGLSEDAYDSYGQEE 320
Cdd:pfam16568   1 YEEYGYDDGYGGEYDEQSYESYDNSYYSQAQSDPEYYDYGHGESQESYDSYGQEE 55
Qua1 pfam16274
Qua1 domain; This domain, approximately 40 residues in length, is mainly found in KH-domain ...
 4-53 2.69e-25

Qua1 domain; This domain, approximately 40 residues in length, is mainly found in KH-domain containing, RNA-binding, signal transduction-associated protein 1 from yeast to human. It forms a homodimer composed of a perpendicular interaction of two helical hairpins, and the Qua1 domain is sufficient for homodimerization which is required for the regulation of alternative splicing.


Pssm-ID: 465079  Cd Length: 52  Bit Score: 96.34  E-value: 2.69e-25
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 117647236    4 KYLPELMAEKDSLDPSFTHALRLVNREIEKFQKGEGK--EEEKYIDVVINKN 53
Cdd:pfam16274   1 KYLPELMAEKDSLDPSFTHAMQLLSAEIEKIQKGESKkdDEEKYLDLFSNKN 52
MSL5 COG5176
Splicing factor (branch point binding protein) [RNA processing and modification];
55-176 4.78e-14

Splicing factor (branch point binding protein) [RNA processing and modification];


Pssm-ID: 227503 [Multi-domain]  Cd Length: 269  Bit Score: 71.15  E-value: 4.78e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117647236  55 KLGQKVLIPVKQFPKFNFVGKLLGPRGNSLKRLQEETLTKMSILGKGSMrdkaKEEELRKSGEAKYFHLNDDLHVLIEVF 134
Cdd:COG5176  147 KYQNKIYIPVQEYPESNFVGLLIGPRGSTLKQLERISRAKIAIRGSGSV----KEGKISSDTPESLKNAEAVLHCLIEAD 222

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|..
gi 117647236 135 APPAEAYARMGHALEEIKKFLIPDYNDEIRQAQLQELTYLNG 176
Cdd:COG5176  223 SEDKICRLIKSQLNAIREARRNPEGQNDLKRFQLRWLAHLNG 264
KH smart00322
K homology RNA-binding domain;
58-102 8.35e-04

K homology RNA-binding domain;


Pssm-ID: 197652 [Multi-domain]  Cd Length: 68  Bit Score: 37.27  E-value: 8.35e-04
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*
gi 117647236    58 QKVLIPVkqfpkfNFVGKLLGPRGNSLKRLQEETLTKMSILGKGS 102
Cdd:smart00322   5 IEVLIPA------DKVGLIIGKGGSTIKKIEEETGVKIDIPGPGS 43
KH_1 pfam00013
KH domain; KH motifs bind RNA in vitro. Autoantibodies to Nova, a KH domain protein, cause ...
 58-102 6.45e-03

KH domain; KH motifs bind RNA in vitro. Autoantibodies to Nova, a KH domain protein, cause paraneoplastic opsoclonus ataxia.


Pssm-ID: 459630 [Multi-domain]  Cd Length: 65  Bit Score: 34.95  E-value: 6.45e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 117647236   58 QKVLIPVKQfpkfnfVGKLLGPRGNSLKRLQEETLTKMSILGKGS 102
Cdd:pfam00013   2 VEILVPSSL------VGLIIGKGGSNIKEIREETGAKIQIPPSES 40
 
Name Accession Description Interval E-value
KH-I_KHDRBS3 cd22470
type I K homology (KH) RNA-binding domain found in KH domain-containing, RNA-binding, signal ...
 48-160 2.38e-70

type I K homology (KH) RNA-binding domain found in KH domain-containing, RNA-binding, signal transduction-associated protein 3 (KHDRBS3) and similar proteins; KHDRBS3, also called RNA-binding protein T-Star, or Sam68-like mammalian protein 2, or SLM-2, or Sam68-like phosphotyrosine protein, is an RNA-binding protein that plays a role in the regulation of alternative splicing and influences mRNA splice site selection and exon inclusion. It binds optimally to RNA containing 5'-[AU]UAA-3' as a bipartite motif spaced by more than 15 nucleotides. It also binds poly(A). KHDRBS3 may play a role as a negative regulator of cell growth.


Pssm-ID: 411898 [Multi-domain]  Cd Length: 113  Bit Score: 214.91  E-value: 2.38e-70
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117647236  48 VVINKNMKLGQKVLIPVKQFPKFNFVGKLLGPRGNSLKRLQEETLTKMSILGKGSMRDKAKEEELRKSGEAKYFHLNDDL 127
Cdd:cd22470    1 VVINKNMKLGQKVLIPVKQFPKFNFVGKLLGPRGNSLKRLQEETLTKMSILGKGSMRDKAKEEELRKSGEAKYFHLNDDL 80

                         90       100       110
                 ....*....|....*....|....*....|...
gi 117647236 128 HVLIEVFAPPAEAYARMGHALEEIKKFLIPDYN 160
Cdd:cd22470   81 HVLIEVFAPPAEAYARMGHALEEIKKFLIPDYN 113
KH-I_KHDRBS cd22384
type I K homology (KH) RNA-binding domain found in the KH domain-containing, RNA-binding, ...
 52-153 5.30e-69

type I K homology (KH) RNA-binding domain found in the KH domain-containing, RNA-binding, signal transduction-associated protein (KHDRBS) family; The KHDRBS family includes three members, KHDRBS1-3. KHDRBS1, also called GAP-associated tyrosine phosphoprotein p62, or Src-associated in mitosis 68 kDa protein, or Sam68, or p21 Ras GTPase-activating protein-associated p62, or p68, is an RNA-binding protein that plays a role in the regulation of alternative splicing and influences mRNA splice site selection and exon inclusion. It binds to RNA containing 5'-[AU]UAA-3' as a bipartite motif spaced by more than 15 nucleotides. It also binds poly(A). KHDRBS1 acts as a putative regulator of mRNA stability and/or translation rates and mediates mRNA nuclear export. It is recruited and tyrosine phosphorylated by several receptor systems, for example the T-cell, leptin and insulin receptors. KHDRBS2, also called Sam68-like mammalian protein 1, or SLM-1, is an RNA-binding protein that plays a role in the regulation of alternative splicing and influences mRNA splice site selection and exon inclusion. It binds both poly(A) and poly(U) homopolymers. KHDRBS2 may function as an adapter protein for Src kinases during mitosis. KHDRBS3, also called RNA-binding protein T-Star, or Sam68-like mammalian protein 2, or SLM-2, or Sam68-like phosphotyrosine protein, is an RNA-binding protein that plays a role in the regulation of alternative splicing and influences mRNA splice site selection and exon inclusion. It binds optimally to RNA containing 5'-[AU]UAA-3' as a bipartite motif spaced by more than 15 nucleotides. It also binds poly(A). KHDRBS3 may play a role as a negative regulator of cell growth.


Pssm-ID: 411812 [Multi-domain]  Cd Length: 102  Bit Score: 210.99  E-value: 5.30e-69
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117647236  52 KNMKLGQKVLIPVKQFPKFNFVGKLLGPRGNSLKRLQEETLTKMSILGKGSMRDKAKEEELRKSGEAKYFHLNDDLHVLI 131
Cdd:cd22384    1 KPIKLSEKVLIPVKEFPKFNFVGKLLGPRGNTLKRLQEETGTKMSILGKGSMRDKAKEEELRKSGDPKYAHLNEDLHVLI 80

                         90       100
                 ....*....|....*....|..
gi 117647236 132 EVFAPPAEAYARMGHALEEIKK 153
Cdd:cd22384   81 EAFAPPAEAYARLAHALAELRK 102
KH-I_KHDRBS2 cd22469
type I K homology (KH) RNA-binding domain found in KH domain-containing, RNA-binding, signal ...
 51-167 5.48e-66

type I K homology (KH) RNA-binding domain found in KH domain-containing, RNA-binding, signal transduction-associated protein 2 (KHDRBS2) and similar proteins; KHDRBS2, also called Sam68-like mammalian protein 1, or SLM-1, is an RNA-binding protein that plays a role in the regulation of alternative splicing and influences mRNA splice site selection and exon inclusion. It binds both poly(A) and poly(U) homopolymers. KHDRBS2 may function as an adapter protein for Src kinases during mitosis.


Pssm-ID: 411897 [Multi-domain]  Cd Length: 118  Bit Score: 203.82  E-value: 5.48e-66
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117647236  51 NKNMKLGQKVLIPVKQFPKFNFVGKLLGPRGNSLKRLQEETLTKMSILGKGSMRDKAKEEELRKSGEAKYFHLNDDLHVL 130
Cdd:cd22469    2 NKNIKLSERVLIPVKQYPKFNFVGKLLGPRGNSLKRLQEETGAKMSILGKGSMRDKAKEEELRKSGEAKYAHLSDELHVL 81

                         90       100       110
                 ....*....|....*....|....*....|....*..
gi 117647236 131 IEVFAPPAEAYARMGHALEEIKKFLIPDYNDEIRQAQ 167
Cdd:cd22469   82 IEVFAPPGEAYSRMSHALEEIKKFLVPDYNDEIRQEQ 118
KH-I_KHDRBS1 cd22468
type I K homology (KH) RNA-binding domain found in KH domain-containing, RNA-binding, signal ...
 52-157 6.43e-60

type I K homology (KH) RNA-binding domain found in KH domain-containing, RNA-binding, signal transduction-associated protein 1 (KHDRBS1) and similar proteins; KHDRBS1, also called GAP-associated tyrosine phosphoprotein p62, or Src-associated in mitosis 68 kDa protein, or Sam68, or p21 Ras GTPase-activating protein-associated p62, or p68, is an RNA-binding protein that plays a role in the regulation of alternative splicing and influences mRNA splice site selection and exon inclusion. It binds to RNA containing 5'-[AU]UAA-3' as a bipartite motif spaced by more than 15 nucleotides. It also binds poly(A). KHDRBS1 acts as a putative regulator of mRNA stability and/or translation rates and mediates mRNA nuclear export. It is recruited and tyrosine phosphorylated by several receptor systems, for example the T-cell, leptin and insulin receptors.


Pssm-ID: 411896 [Multi-domain]  Cd Length: 106  Bit Score: 187.92  E-value: 6.43e-60
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117647236  52 KNMKLGQKVLIPVKQFPKFNFVGKLLGPRGNSLKRLQEETLTKMSILGKGSMRDKAKEEELRKSGEAKYFHLNDDLHVLI 131
Cdd:cd22468    1 KNMKLKERILIPVKQYPKFNFVGKILGPQGNTIKRLQEETGAKISVLGKGSMRDKAKEEELRKGGDPKYAHLNMDLHVFI 80

                         90       100
                 ....*....|....*....|....*.
gi 117647236 132 EVFAPPAEAYARMGHALEEIKKFLIP 157
Cdd:cd22468   81 EVFGPPCEAYARMAHAMEEVKKFLVP 106
KH-I_Hqk_like cd22383
type I K homology (KH) RNA-binding domain found in protein quaking (Hqk) family; The Hqk ...
 55-157 1.85e-39

type I K homology (KH) RNA-binding domain found in protein quaking (Hqk) family; The Hqk family includes Hqk and protein held out wings (how) found in Drosophila. Hqk, also called HqkI, is an RNA-binding protein that plays a central role in myelinization. It binds to the 5'-NACUAAY-N(1,20)-UAAY-3' RNA core sequence and regulates target mRNA stability. It acts by regulating pre-mRNA splicing, mRNA export and protein translation. Hqk is a regulator of oligodendrocyte differentiation and maturation in the brain that may play a role in myelin and oligodendrocyte dysfunction in schizophrenia. How, also called KH domain protein KH93F, or protein muscle-specific, or protein Struthio, or protein wings held out (who), or Quaking-related 93F (qkr93F), is an RNA-binding protein involved in the control of muscular and cardiac activity. It is required for integrin-mediated cell-adhesion in wing blade. It plays essential roles during embryogenesis, in late stages of somatic muscle development, for myotube migration and during metamorphosis for muscle reorganization.


Pssm-ID: 411811 [Multi-domain]  Cd Length: 101  Bit Score: 135.18  E-value: 1.85e-39
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117647236  55 KLGQKVLIPVKQFPKFNFVGKLLGPRGNSLKRLQEETLTKMSILGKGSMRDKAKEEELRksGEAKYFHLNDDLHVLIEVF 134
Cdd:cd22383    1 KLSEKVYVPVDEYPDYNFVGRILGPRGMTAKQLEQDTGCKIMIRGKGSMRDKKKEEANR--GKPNWEHLNDDLHVLITVE 78

                         90       100
                 ....*....|....*....|...
gi 117647236 135 APPAEAYARMGHALEEIKKFLIP 157
Cdd:cd22383   79 DTENRAHIKLAKAVEEVKKLLIP 101
KH-I_Hqk cd22465
type I K homology (KH) RNA-binding domain found in protein quaking (Hqk) and similar proteins; ...
 55-157 1.39e-31

type I K homology (KH) RNA-binding domain found in protein quaking (Hqk) and similar proteins; Hqk, also called HqkI, is an RNA-binding protein that plays a central role in myelinization. It binds to the 5'-NACUAAY-N(1,20)-UAAY-3' RNA core sequence and regulates target mRNA stability. It acts by regulating pre-mRNA splicing, mRNA export and protein translation. Hqk is a regulator of oligodendrocyte differentiation and maturation in the brain that may play a role in myelin and oligodendrocyte dysfunction in schizophrenia.


Pssm-ID: 411893 [Multi-domain]  Cd Length: 103  Bit Score: 114.65  E-value: 1.39e-31
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117647236  55 KLGQKVLIPVKQFPKFNFVGKLLGPRGNSLKRLQEETLTKMSILGKGSMRDKAKEEELRksGEAKYFHLNDDLHVLIEVF 134
Cdd:cd22465    1 QLQEKLYVPVKEYPDFNFVGRILGPRGLTAKQLEAETGCKIMVRGKGSMRDKKKEEQNR--GKPNWEHLNEDLHVLITVE 78

                         90       100
                 ....*....|....*....|...
gi 117647236 135 APPAEAYARMGHALEEIKKFLIP 157
Cdd:cd22465   79 DAQNRAEIKLKRAVEEVKKLLVP 101
KH-I_HOW cd22466
type I K homology (KH) RNA-binding domain found in Drosophila protein held out wings (how) and ...
 56-157 3.22e-31

type I K homology (KH) RNA-binding domain found in Drosophila protein held out wings (how) and similar proteins; How, also called KH domain protein KH93F, or protein muscle-specific, or protein Struthio, or protein wings held out (who), or Quaking-related 93F (qkr93F), is an RNA-binding protein involved in the control of muscular and cardiac activity. It is required for integrin-mediated cell-adhesion in wing blade. It plays essential roles during embryogenesis, in late stages of somatic muscle development, for myotube migration and during metamorphosis for muscle reorganization.


Pssm-ID: 411894 [Multi-domain]  Cd Length: 105  Bit Score: 113.86  E-value: 3.22e-31
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117647236  56 LGQKVLIPVKQFPKFNFVGKLLGPRGNSLKRLQEETLTKMSILGKGSMRDKAKEEELRksGEAKYFHLNDDLHVLIEVFA 135
Cdd:cd22466    6 LSEKVYVPVKEHPDYNFVGRILGPRGMTAKQLEQETGCKIMVRGKGSMRDKKKEDLNR--GKPNWEHLNDELHVLITVED 83

                         90       100
                 ....*....|....*....|..
gi 117647236 136 PPAEAYARMGHALEEIKKFLIP 157
Cdd:cd22466   84 TENRAKVKLQRAVEEVRKLLVP 105
Sam68-YY pfam16568
Tyrosine-rich domain of Sam68; Sam68-YY is a short tyrosine-rich domain on Src-associated in ...
 266-320 3.40e-28

Tyrosine-rich domain of Sam68; Sam68-YY is a short tyrosine-rich domain on Src-associated in mitosis, 68 kDa protein (Sam68), a protein that regulates TCF-1 alternative splicing. It is a crucial binding-partner of the APC-Arm domain that forms a superhelix with a positively charged groove, the surface-residues of which groove form numerous interactions with Sam68-YY to fix it in a bent conformation. APC-Arm is the armadillo repeat domain of the tumour-suppressor protein adenomatous polyposis coli or APC. APC plays plays important roles in Wnt signalling and other cellular processes.


Pssm-ID: 465182  Cd Length: 55  Bit Score: 104.07  E-value: 3.40e-28
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 117647236  266 YGEYDYDDGYGTAYDEQSYDSYDNSYSTPAQSAADYYDYGHGLSEDAYDSYGQEE 320
Cdd:pfam16568   1 YEEYGYDDGYGGEYDEQSYESYDNSYYSQAQSDPEYYDYGHGESQESYDSYGQEE 55
KH-I_SPIN1_like cd22467
type I K homology (KH) RNA-binding domain found in Oryza sativa SPL11-interacting protein 1 ...
 58-157 1.08e-26

type I K homology (KH) RNA-binding domain found in Oryza sativa SPL11-interacting protein 1 (SPIN1) and similar proteins; SPIN1 is a K homology domain protein negatively regulated and ubiquitinated by the E3 ubiquitin ligase SPL11. It is involved in flowering time control in rice. SPIN1 binds DNA and RNA in vitro.


Pssm-ID: 411895  Cd Length: 101  Bit Score: 101.41  E-value: 1.08e-26
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117647236  58 QKVLIPVKQFPKFNFVGKLLGPRGNSLKRLQEETLTKMSILGKGSMRDKAKEEELRksGEAKYFHLNDDLHVLIEVFAPP 137
Cdd:cd22467    4 LRLDVPVDKYPNFNFVGRILGPRGNSLKRVEATTGCRVFIRGRGSIKDTAKEEKLR--DKPGYEHLNEPLHVLIEAELPA 81

                         90       100
                 ....*....|....*....|
gi 117647236 138 AEAYARMGHALEEIKKFLIP 157
Cdd:cd22467   82 NIIDARLQHAQEIIEDLLKP 101
Qua1 pfam16274
Qua1 domain; This domain, approximately 40 residues in length, is mainly found in KH-domain ...
 4-53 2.69e-25

Qua1 domain; This domain, approximately 40 residues in length, is mainly found in KH-domain containing, RNA-binding, signal transduction-associated protein 1 from yeast to human. It forms a homodimer composed of a perpendicular interaction of two helical hairpins, and the Qua1 domain is sufficient for homodimerization which is required for the regulation of alternative splicing.


Pssm-ID: 465079  Cd Length: 52  Bit Score: 96.34  E-value: 2.69e-25
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 117647236    4 KYLPELMAEKDSLDPSFTHALRLVNREIEKFQKGEGK--EEEKYIDVVINKN 53
Cdd:pfam16274   1 KYLPELMAEKDSLDPSFTHAMQLLSAEIEKIQKGESKkdDEEKYLDLFSNKN 52
KH-I_BBP cd02395
type I K homology (KH) RNA-binding domain found in yeast branchpoint-bridging protein (BBP) ...
 55-156 7.74e-23

type I K homology (KH) RNA-binding domain found in yeast branchpoint-bridging protein (BBP) and similar proteins; Yeast BBP, also called mud synthetic-lethal 5 protein, or splicing factor 1, or zinc finger protein BBP, is a mammalian splicing factor SF1 ortholog. It is involved in protein-protein interactions that bridge the 3' and 5' splice-site ends of the intron during the early steps of yeast pre-mRNA splicing. BBP interacts specifically with the pre-mRNA branchpoint sequence UACUAAC.


Pssm-ID: 411805 [Multi-domain]  Cd Length: 92  Bit Score: 91.12  E-value: 7.74e-23
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117647236  55 KLGQKVLIPVKQFPKFNFVGKLLGPRGNSLKRLQEETLTKMSILGKGSMRDKAKEEELRKSGEAkyfhlNDDLHVLIEvf 134
Cdd:cd02395    1 KKQRKIYIPVDEYPDYNFIGLIIGPRGNTQKRMEKESGAKIAIRGKGSVKEGKGRSDPQPDPDE-----EEDLHVLIT-- 73

                         90       100
                 ....*....|....*....|..
gi 117647236 135 appAEAYARMGHALEEIKKFLI 156
Cdd:cd02395   74 ---ADTEEKVDKAAKLIEKLLI 92
KH-I_SF1 cd22382
type I K homology (KH) RNA-binding domain found in splicing factor 1 (SF1) and similar ...
 55-153 9.01e-15

type I K homology (KH) RNA-binding domain found in splicing factor 1 (SF1) and similar proteins; SF1, also called branch point-binding protein, or BBP, or transcription factor ZFM1, or zinc finger gene in MEN1 locus, or zinc finger protein 162, is necessary for the ATP-dependent first step of spliceosome assembly. Binds to the intron branch point sequence (BPS) 5'-UACUAAC-3' of the pre-mRNA. It may act as transcription repressor.


Pssm-ID: 411810 [Multi-domain]  Cd Length: 93  Bit Score: 68.87  E-value: 9.01e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117647236  55 KLGQKVLIPVKQFPKFNFVGKLLGPRGNSLKRLQEETLTKMSILGKGSmrdkAKEEELRKSGEAKYFHLNDDLHVLIEvf 134
Cdd:cd22382    1 RVSDKVMIPQEEYPDINFVGLLIGPRGNTLKKIEKETGAKIMIRGKGS----VKEGKVGRKDGQPLPGEDEPLHALVT-- 74

                         90
                 ....*....|....*....
gi 117647236 135 APPAEAYARMGHALEEIKK 153
Cdd:cd22382   75 ANTAESVKKAVDKIKEIIK 93
MSL5 COG5176
Splicing factor (branch point binding protein) [RNA processing and modification];
55-176 4.78e-14

Splicing factor (branch point binding protein) [RNA processing and modification];


Pssm-ID: 227503 [Multi-domain]  Cd Length: 269  Bit Score: 71.15  E-value: 4.78e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117647236  55 KLGQKVLIPVKQFPKFNFVGKLLGPRGNSLKRLQEETLTKMSILGKGSMrdkaKEEELRKSGEAKYFHLNDDLHVLIEVF 134
Cdd:COG5176  147 KYQNKIYIPVQEYPESNFVGLLIGPRGSTLKQLERISRAKIAIRGSGSV----KEGKISSDTPESLKNAEAVLHCLIEAD 222

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|..
gi 117647236 135 APPAEAYARMGHALEEIKKFLIPDYNDEIRQAQLQELTYLNG 176
Cdd:COG5176  223 SEDKICRLIKSQLNAIREARRNPEGQNDLKRFQLRWLAHLNG 264
KH-I_KHDC4_rpt2 cd22386
first type I K homology (KH) RNA-binding domain found in KH homology domain-containing protein ...
 59-143 1.66e-06

first type I K homology (KH) RNA-binding domain found in KH homology domain-containing protein 4 (KHDC4) and similar proteins; KHDC4, also called Brings lots of money 7 (Blom7), or pre-mRNA splicing factor protein KHDC4, is an RNA-binding protein involved in pre-mRNA splicing. It interacts with the PRP19C/Prp19 complex/NTC/Nineteen complex which is part of the spliceosome. KHDC4 binds preferentially RNA with A/C rich sequences and poly-C stretches. KHDC4 contains two type I K homology (KH) RNA-binding domains. The model corresponds to the second one.


Pssm-ID: 411814 [Multi-domain]  Cd Length: 102  Bit Score: 46.01  E-value: 1.66e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 117647236  59 KVLIPVKQFPK-FNFVGKLLGPRGNSLKRLQEETLTKMSILGKGSmrdKAKEEElrkSGEAKyfhlNDDLHVLIEvfAPP 137
Cdd:cd22386    6 KVFVGLEHAPPgFNVRGKLIGPGGSNVKHIQQETGAKVQLRGKGS---GFIEPA---SGREA----DEPLHLLIS--HPD 73


                 ....*.
gi 117647236 138 AEAYAR 143
Cdd:cd22386   74 PEGLQQ 79
KH-I_IGF2BP1_rpt2 cd22493
second type I K homology (KH) RNA-binding domain found in insulin-like growth factor 2 ...
 62-118 2.93e-04

second type I K homology (KH) RNA-binding domain found in insulin-like growth factor 2 mRNA-binding protein 1 (IGF2BP1) and similar proteins; IGF2BP1, also called IGF2 mRNA-binding protein 1 (IMP-1), or coding region determinant-binding protein (CRD-BP), or IGF-II mRNA-binding protein 1, or VICKZ family member 1 (VICKZ1), or zipcode-binding protein 1 (ZBP-1), is an RNA-binding factor that recruits target transcripts to cytoplasmic protein-RNA complexes (mRNPs). It functions by binding to the 5' UTR of the insulin-like growth factor 2 (IGF2) mRNA and regulating IGF2 translation. It regulates localized beta-actin/ACTB mRNA translation, a crucial process for cell polarity, cell migration and neurite outgrowth. IGF2BP1 can form homodimers and heterodimers with IGF2BP1 and IGF2BP3. It contains four K-homology (KH) RNA-binding domains which are important in RNA binding and are known to be involved in RNA synthesis and metabolism. The model corresponds to the second one.


Pssm-ID: 411921  Cd Length: 97  Bit Score: 39.66  E-value: 2.93e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 117647236  62 IPVKQFPKFNFVGKLLGPRGNSLKRLQEETLTKMSILG---------------KGSMRD--KAKEEELRKSGEA 118
Cdd:cd22493    5 VPLKILAHNNFVGRLIGKEGRNLKKVEQDTETKITISPlqdltlynpertitvKGSIEAccRAEQEIMKKVREA 78
KH smart00322
K homology RNA-binding domain;
58-102 8.35e-04

K homology RNA-binding domain;


Pssm-ID: 197652 [Multi-domain]  Cd Length: 68  Bit Score: 37.27  E-value: 8.35e-04
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*
gi 117647236    58 QKVLIPVkqfpkfNFVGKLLGPRGNSLKRLQEETLTKMSILGKGS 102
Cdd:smart00322   5 IEVLIPA------DKVGLIIGKGGSTIKKIEEETGVKIDIPGPGS 43
KH-I cd00105
K homology (KH) RNA-binding domain, type I; KH binds single-stranded RNA or DNA. It is found ...
 59-102 9.28e-04

K homology (KH) RNA-binding domain, type I; KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that belong to different protein folds, but they share a single KH motif. The KH motif is folded into a beta alpha alpha beta unit. In addition to the core, type II KH domains (e.g. ribosomal protein S3) include an N-terminal extension and type I KH domains (e.g. hnRNP K) contain a C-terminal extension. Some KH-I superfamily members contain a divergent KH domain that lacks the RNA-binding GXXG motif. Some others have a mutated GXXG motif which may or may not have nucleic acid binding ability.


Pssm-ID: 411802 [Multi-domain]  Cd Length: 63  Bit Score: 37.28  E-value: 9.28e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....
gi 117647236  59 KVLIPVKqfpkfnFVGKLLGPRGNSLKRLQEETLTKMSILGKGS 102
Cdd:cd00105    2 EIEVPSE------LVGLIIGKGGSTIKEIEEETGARIQIPKEGE 39
KH-I_IGF2BP3_rpt2 cd22495
second type I K homology (KH) RNA-binding domain found in insulin-like growth factor 2 ...
 63-97 1.32e-03

second type I K homology (KH) RNA-binding domain found in insulin-like growth factor 2 mRNA-binding protein 3 (IGF2BP3) and similar proteins; IGF2BP3, also called IGF2 mRNA-binding protein 3 (IMP-3), or hepatocellular carcinoma autoantigen p62, or IGF-II mRNA-binding protein 3, or VICKZ family member 3 (VICKZ3), or KH domain-containing protein overexpressed in cancer, or KOC, is primarily found in the nucleolus, where it can bind to the 5' UTR of the insulin-like growth factor II leader 3 mRNA and may repress translation of insulin-like growth factor II during late development. It acts as an RNA-binding factor that may recruit target transcripts to cytoplasmic protein-RNA complexes (mRNPs). It also modulates the rate and location at which target transcripts encounter the translational apparatus and shields them from endonuclease attacks or microRNA-mediated degradation. IGF2BP3 binds to the 3'-UTR of CD44 mRNA and stabilizes it, hence promotes cell adhesion and invadopodia formation in cancer cells. It also binds to beta-actin/ACTB and MYC transcripts. IGF2BP3 can form homooligomers and heterooligomers with IGF2BP1 and IGF2BP2 in an RNA-dependent manner. IGF2BP3 contains four K-homology (KH) RNA-binding domains which are important in RNA binding and are known to be involved in RNA synthesis and metabolism. The model corresponds to the second one.


Pssm-ID: 411923  Cd Length: 77  Bit Score: 37.33  E-value: 1.32e-03
                         10        20        30
                 ....*....|....*....|....*....|....*
gi 117647236  63 PVKQFPKFNFVGKLLGPRGNSLKRLQEETLTKMSI 97
Cdd:cd22495    1 PLKILAHNNFVGRLIGKEGRNLKKIEQDTDTKITI 35
KH-I_IGF2BP_rpt2 cd22401
second type I K homology (KH) RNA-binding domain found in the insulin-like growth factor 2 ...
 71-97 5.59e-03

second type I K homology (KH) RNA-binding domain found in the insulin-like growth factor 2 mRNA-binding protein (IGF2BP) family; The IGF2BP family includes three members: IGF2BP1/IMP-1/ CRD-BP/ VICKZ1, IGF2BP2/IMP-2/ VICKZ2, and IGF2BP3/IMP-3/VICKZ3, which are RNA-binding factors that recruit target transcripts to cytoplasmic protein-RNA complexes (mRNPs). They function by binding to the 5' UTR of the insulin-like growth factor 2 (IGF2) mRNA and regulating IGF2 translation. IGF2BP proteins contain four K-homology (KH) RNA-binding domains which are important in RNA binding and are known to be involved in RNA synthesis and metabolism. The model corresponds to the second one.


Pssm-ID: 411829 [Multi-domain]  Cd Length: 72  Bit Score: 35.28  E-value: 5.59e-03
                         10        20
                 ....*....|....*....|....*..
gi 117647236  71 NFVGKLLGPRGNSLKRLQEETLTKMSI 97
Cdd:cd22401    9 NLCGRLIGKDGRNIKKIMEDTNTKITI 35
KH_1 pfam00013
KH domain; KH motifs bind RNA in vitro. Autoantibodies to Nova, a KH domain protein, cause ...
 58-102 6.45e-03

KH domain; KH motifs bind RNA in vitro. Autoantibodies to Nova, a KH domain protein, cause paraneoplastic opsoclonus ataxia.


Pssm-ID: 459630 [Multi-domain]  Cd Length: 65  Bit Score: 34.95  E-value: 6.45e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 117647236   58 QKVLIPVKQfpkfnfVGKLLGPRGNSLKRLQEETLTKMSILGKGS 102
Cdd:pfam00013   2 VEILVPSSL------VGLIIGKGGSNIKEIREETGAKIQIPPSES 40
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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