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.

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 5730027    102 KYLPELMAEKDSLDPSFTHAMQLLTAEIEKIQKGDSKKDDEENYLDLFSHKN 153
Cdd:pfam16274   1 KYLPELMAEKDSLDPSFTHAMQLLSAEIEKIQKGESKKDDEEKYLDLFSNKN 52

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.

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 5730027    102 KYLPELMAEKDSLDPSFTHAMQLLTAEIEKIQKGDSKKDDEENYLDLFSHKN 153
Cdd:pfam16274   1 KYLPELMAEKDSLDPSFTHAMQLLSAEIEKIQKGESKKDDEEKYLDLFSNKN 52

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

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5730027  155 KLKERVLIPVKQYPKFNFVGKILGPQGNTIKRLQEETGAKISVLGKGSMrdkaKEEELRKGGDPKYAHLNMDLHVFIE-- 232
Cdd:COG5176 147 KYQNKIYIPVQEYPESNFVGLLIGPRGSTLKQLERISRAKIAIRGSGSV----KEGKISSDTPESLKNAEAVLHCLIEad 222

                        90       100       110       120
                ....*....|....*....|....*....|....*....|....
gi 5730027  233 VFGPPCEAYALMAHAMEEVKKflVPDMMDDICQEQFLELSYLNG 276
Cdd:COG5176 223 SEDKICRLIKSQLNAIREARR--NPEGQNDLKRFQLRWLAHLNG 264

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

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 5730027    157 KERVLIPVKQypkfnfVGKILGPQGNTIKRLQEETGAKISVLGKGS 202
Cdd:pfam00013   1 TVEILVPSSL------VGLIIGKGGSNIKEIREETGAKIQIPPSES 40

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.

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5730027  152 KNMKLKERVLIPVKQYPKFNFVGKILGPQGNTIKRLQEETGAKISVLGKGSMRDKAKEEELRKGGDPKYAHLNMDLHVFI 231
Cdd:cd22384   1 KPIKLSEKVLIPVKEFPKFNFVGKLLGPRGNTLKRLQEETGTKMSILGKGSMRDKAKEEELRKSGDPKYAHLNEDLHVLI 80

                        90       100
                ....*....|....*....|..
gi 5730027  232 EVFGPPCEAYALMAHAMEEVKK 253
Cdd:cd22384  81 EAFAPPAEAYARLAHALAELRK 102

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.

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5730027  150 SHKNMKLKERVLIPVKQYPKFNFVGKILGPQGNTIKRLQEETGAKISVLGKGSMRDKAKEEELRKGGDPKYAHLNMDLHV 229
Cdd:cd22470   3 INKNMKLGQKVLIPVKQFPKFNFVGKLLGPRGNSLKRLQEETLTKMSILGKGSMRDKAKEEELRKSGEAKYFHLNDDLHV 82

                        90       100
                ....*....|....*....|....*....
gi 5730027  230 FIEVFGPPCEAYALMAHAMEEVKKFLVPD 258
Cdd:cd22470  83 LIEVFAPPAEAYARMGHALEEIKKFLIPD 111

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.

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5730027  155 KLKERVLIPVKQYPKFNFVGKILGPQGNTIKRLQEETGAKISVLGKGSMRDKAKEEELRkgGDPKYAHLNMDLHVFIEVF 234
Cdd:cd22465   1 QLQEKLYVPVKEYPDFNFVGRILGPRGLTAKQLEAETGCKIMVRGKGSMRDKKKEEQNR--GKPNWEHLNEDLHVLITVE 78

                        90       100
                ....*....|....*....|...
gi 5730027  235 GPPCEAYALMAHAMEEVKKFLVP 257
Cdd:cd22465  79 DAQNRAEIKLKRAVEEVKKLLVP 101

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.

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 5730027    102 KYLPELMAEKDSLDPSFTHAMQLLTAEIEKIQKGDSKKDDEENYLDLFSHKN 153
Cdd:pfam16274   1 KYLPELMAEKDSLDPSFTHAMQLLSAEIEKIQKGESKKDDEEKYLDLFSNKN 52

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.

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5730027  155 KLKERVLIPVKQYPKFNFVGKILGPQGNTIKRLQEETGAKISVLGKGSMRDKAKEEELRKGGDpkyahLNMDLHVFIEVF 234
Cdd:cd02395   1 KKQRKIYIPVDEYPDYNFIGLIIGPRGNTQKRMEKESGAKIAIRGKGSVKEGKGRSDPQPDPD-----EEEDLHVLITAD 75

                        90       100
                ....*....|....*....|..
gi 5730027  235 GPPCeayalMAHAMEEVKKFLV 256
Cdd:cd02395  76 TEEK-----VDKAAKLIEKLLI 92

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.

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5730027  155 KLKERVLIPVKQYPKFNFVGKILGPQGNTIKRLQEETGAKISVLGKGSmrdkAKEEELRKGGDPKYAHLNMDLHVFIEvf 234
Cdd:cd22382   1 RVSDKVMIPQEEYPDINFVGLLIGPRGNTLKKIEKETGAKIMIRGKGS----VKEGKVGRKDGQPLPGEDEPLHALVT-- 74

                        90
                ....*....|....*....
gi 5730027  235 gppceayalmAHAMEEVKK 253
Cdd:cd22382  75 ----------ANTAESVKK 83

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.

                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*....
gi 5730027  155 KLKERVLIPVKQYPK-FNFVGKILGPQGNTIKRLQEETGAKISVLGKGS 202
Cdd:cd22386   2 YYQEKVFVGLEHAPPgFNVRGKLIGPGGSNVKHIQQETGAKVQLRGKGS 50

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

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 5730027    157 KERVLIPVKQypkfnfVGKILGPQGNTIKRLQEETGAKISVLGKGS 202
Cdd:pfam00013   1 TVEILVPSSL------VGLIIGKGGSNIKEIREETGAKIQIPPSES 40

first type I K homology (KH) RNA-binding domain found in Arabidopsis thaliana RNA-binding KH domain-containing protein PEPPER and similar proteins; The family includes a group of plant RNA-binding KH domain-containing proteins, such as PEPPER, flowering locus K homology domain protein (FLK), RNA-binding KH domain-containing protein RCF3 and KH domain-containing protein HEN4. PEPPER regulates vegetative and gynoecium development. It acts as a positive regulator of the central floral repressor FLOWERING LOCUS C. In concert with HUA2, PEPPER antagonizes FLK by positively regulating FLC probably at transcriptional and post-transcriptional levels, and thus acts as a negative regulator of flowering. FLK, also called flowering locus KH domain protein, regulates positively flowering by repressing FLC expression and post-transcriptional modification. PEPPER and FLK contain three K-homology (KH) RNA-binding domains. RCF3, also called protein ENHANCED STRESS RESPONSE 1 (ESR1), or protein HIGH OSMOTIC STRESS GENE EXPRESSION 5 (HOS5), or protein REGULATOR OF CBF GENE EXPRESSION 3, or protein SHINY 1 (SHI1), acts as negative regulator of osmotic stress-induced gene expression. It is involved in the regulation of thermotolerance responses under heat stress. It functions as an upstream regulator of heat stress transcription factor (HSF) genes. HEN4, also called protein HUA ENHANCER 4, plays a role in floral reproductive organ identity in the third whorl and floral determinacy specification by specifically promoting the processing of AGAMOUS (AG) pre-mRNA. It functions in association with HUA1 and HUA2. RCF3 and HEN4 contain five KH RNA-binding domains. The model corresponds to the KH1 domain of PEPPER and FLK, as well as KH1 and KH3 domains of RCF3 and HEN4.

                        10        20        30        40
                ....*....|....*....|....*....|....*....|
gi 5730027  159 RVLIPVKQypkfnfVGKILGPQGNTIKRLQEETGAKISVL 198
Cdd:cd22459   5 RLLCPVSK------AGSVIGKGGEIIKQLRQETGARIKVE 38

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.

                        10        20
                ....*....|....*....|....*..
gi 5730027  171 NFVGKILGPQGNTIKRLQEETGAKISV 197
Cdd:cd22401   9 NLCGRLIGKDGRNIKKIMEDTNTKITI 35

third type I K homology (KH) RNA-binding domain found in the family of neuro-oncological ventral antigen (Nova); The family includes two related neuronal RNA-binding proteins, Nova-1 and Nova-2. Nova-1, also called onconeural ventral antigen 1, or paraneoplastic Ri antigen, or ventral neuron-specific protein 1, may regulate RNA splicing or metabolism in a specific subset of developing neurons. It interacts with RNA containing repeats of the YCAY sequence. It is a brain-enriched splicing factor regulating neuronal alternative splicing. Nova-1 is involved in neurological disorders and carcinogenesis. Nova-2, also called astrocytic NOVA1-like RNA-binding protein, is a neuronal RNA-binding protein expressed in a broader central nervous system (CNS) distribution than Nova-1. It functions in neuronal RNA metabolism. NOVA family proteins contain three K-homology (KH) RNA-binding domains. The model corresponds to the third one.

                        10        20        30
                ....*....|....*....|....*....|.
gi 5730027  171 NFVGKILGPQGNTIKRLQEETGAKISVLGKG 201
Cdd:cd09031  10 NLVGAILGKGGKTLVEIQELTGARIQISKKG 40

first type I K homology (KH) RNA-binding domain found in the FUBP family RNA/DNA-binding proteins; The far upstream element-binding protein (FUBP) family includes FUBP1-3. FUBP1, also called FBP, or FUSE-binding protein 1, or DNA helicase V, or DH V, binds RNA and single-stranded DNA (ssDNA) and may act both as activator and repressor of transcription. It regulates MYC expression by binding to a single-stranded far-upstream element (FUSE) upstream of the MYC promoter. FUBP2, also called FUSE-binding protein 2, or KH type-splicing regulatory protein (KSRP), or p75, is a single-strand nucleic acid binding protein implicated in a variety of cellular processes, including splicing in the nucleus, mRNA decay, maturation of miRNA, and transcriptional control of proto-oncogenes such as c-myc. It regulates the stability and/or translatability of many mRNA species, encoding immune-relevant proteins, either by binding to AU-rich elements (AREs) of mRNA 3'UTR or by facilitating miRNA biogenesis to target mRNA. FUBP3, also called FUSE-binding protein 3, or MARTA2, was previously shown to mediate dendritic targeting of MAP2 mRNA in neurons. It may interact with single-stranded DNA from the far-upstream element (FUSE) and activate gene expression. It is required for beta-actin mRNA localization. It also interacts with fibroblast growth factor 9 (FGF9) 3'-UTR UG repeats and positively controls FGF9 expression through increasing translation of FGF9 mRNA. FUBP proteins contain four K-homology (KH) RNA-binding domains. The model corresponds to the first one.

                        10        20        30        40
                ....*....|....*....|....*....|....*....|..
gi 5730027  156 LKERVLIPVKqypkfnFVGKILGPQGNTIKRLQEETGAKISV 197
Cdd:cd22396   1 VTEEYKVPDK------MVGLIIGRGGEQINRLQAESGAKIQI 36

second type I K homology (KH) RNA-binding domain found in Arabidopsis thaliana RNA-binding KH domain-containing protein PEPPER and similar proteins; The family includes a group of plant RNA-binding KH domain-containing proteins, such as PEPPER, flowering locus K homology domain protein (FLK), RNA-binding KH domain-containing protein RCF3 and KH domain-containing protein HEN4. PEPPER regulates vegetative and gynoecium development. It acts as a positive regulator of the central floral repressor FLOWERING LOCUS C. In concert with HUA2, PEPPER antagonizes FLK by positively regulating FLC probably at transcriptional and post-transcriptional levels, and thus acts as a negative regulator of flowering. FLK, also called flowering locus KH domain protein, regulates positively flowering by repressing FLC expression and post-transcriptional modification. PEPPER and FLK contain three K-homology (KH) RNA-binding domains. RCF3, also called protein ENHANCED STRESS RESPONSE 1 (ESR1), or protein HIGH OSMOTIC STRESS GENE EXPRESSION 5 (HOS5), or protein REGULATOR OF CBF GENE EXPRESSION 3, or protein SHINY 1 (SHI1), acts as negative regulator of osmotic stress-induced gene expression. It is involved in the regulation of thermotolerance responses under heat stress. It functions as an upstream regulator of heat stress transcription factor (HSF) genes. HEN4, also called protein HUA ENHANCER 4, plays a role in floral reproductive organ identity in the third whorl and floral determinacy specification by specifically promoting the processing of AGAMOUS (AG) pre-mRNA. It functions in association with HUA1 and HUA2. RCF3 and HEN4 contain five KH RNA-binding domains. The model corresponds to the KH2 domain of PEPPER and FLK, as well as KH2 and KH4 domains of RCF3 and HEN4.

                        10        20        30        40
                ....*....|....*....|....*....|....*....|...
gi 5730027  159 RVLIPVKQypkfnfVGKILGPQGNTIKRLQEETGAKISVLGKG 201
Cdd:cd22460   3 RLLVASSQ------AGSLIGKGGAIIKQIREESGASVRILPEE 39

sixth type I K homology (KH) RNA-binding domain found in vigilin and similar proteins; Vigilin, also called high density lipoprotein-binding protein, or HDL-binding protein, is a ubiquitous and highly conserved RNA-binding protein that shuttles between nucleus and cytoplasm presumably in contact with RNA molecules. It may be involved in chromosome partitioning at mitosis, facilitating translation and tRNA transport, and control of mRNA metabolism, including estrogen-mediated stabilization of vitellogenin mRNA. Vigilin is up-regulated by cholesterol loading of cells and functions to protect cells from over-accumulation of cholesterol. It may play a role in cell sterol metabolism. Disruption of human vigilin impairs chromosome condensation and segregation. Vigilin has a unique structure of 14-15 consecutively arranged, but non-identical K-homology (KH) domains which apparently mediate RNA-protein binding. The model corresponds to the sixth one.

                        10        20        30
                ....*....|....*....|....*....|
gi 5730027  168 PKFnfVGKILGPQGNTIKRLQEETGAKISV 197
Cdd:cd02394  10 PKF--HGHIIGKGGANIKRIREESGVSIRI 37

type I K homology (KH) RNA-binding domain found in DEAD box protein 43 (DDX43), DEAD box protein 53 (DDX53) and similar proteins; DDX43 (also called cancer/testis antigen 13, or DEAD box protein HAGE, or helical antigen) displays tumor-specific expression. Diseases associated with DDX43 include rheumatoid lung disease. DDX53 (also called cancer-associated gene protein, or cancer/testis antigen 26, or DEAD box protein CAGE) shows high expression level in various tumors and is involved in anti-cancer drug resistance. Both DDX46 and DDX53 are members of the DEAD-box helicases, a diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis and RNA degradation.

                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|
gi 5730027  171 NFVGKILGPQGNTIKRLQEETGAKISVL-----------GKGSMRDKAKE 209
Cdd:cd22430   9 SLVGAVIGRGGSKIRELEESTGSKIKIIkggqeaevkifGSDEAQQKAKE 58

second type I K homology (KH) RNA-binding domain found in Saccharomyces cerevisiae Protein SCP160 and similar proteins; SCP160, also called protein HX, is a new yeast protein associated with the nuclear membrane and the endoplasmic reticulum. It is involved in the control of mitotic chromosome transmission. It is required during cell division for faithful partitioning of the ER-nuclear envelope membranes which enclose the duplicated chromosomes in yeast. SCP160 contains seven K-homology (KH) RNA-binding domains. The model corresponds to the second one.

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 5730027  160 VLIPVkqypkfNFVGKILGPQGNTIKRLQEETGAKISVlgkgsmrdkAKEEElrkggDPKYAHLNMDLHVFIEVFGPPCE 239
Cdd:cd22447   8 VPIPA------STRARIIGKKGANLKQIREKTGVRIDI---------PPRDA-----DAAPADEDDDTMVEVTITGDEFN 67

                        90
                ....*....|...
gi 5730027  240 AYALMAHAMEEVK 252
Cdd:cd22447  68 VQHAKQRIEEIIS 80

second type I K homology (KH) RNA-binding domain found in far upstream element-binding protein 3 (FUBP3) and similar proteins; FUBP3, also called FUSE-binding protein 3, or MARTA2, was previously shown to mediate dendritic targeting of MAP2 mRNA in neurons. It may interact with single-stranded DNA from the far-upstream element (FUSE) and activate gene expression. It is required for beta-actin mRNA localization. It also interacts with fibroblast growth factor 9 (FGF9) 3'-UTR UG repeats and positively controls FGF9 expression through increasing translation of FGF9 mRNA. FUBP3 contains four K-homology (KH) RNA-binding domains. The model corresponds to the second one.

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 5730027  158 ERVLIPVKQypkfnfVGKILGPQGNTIKRLQEETGAKISVLGKGSMRDKAkEEELRKGGDP 218
Cdd:cd22483   7 QEILIPASK------VGLVIGKGGETIKQLQERTGVKMIMIQDGPLPTGA-DKPLRITGDP 60

first type I K homology (KH) RNA-binding domain found in heterogeneous nuclear ribonucleoprotein K (hnRNP K) and similar proteins; hnRNP K, also called transformation up-regulated nuclear protein (TUNP), is a pre-mRNA binding protein that binds tenaciously to poly(C) sequences. It may be involved in the nuclear metabolism of hnRNAs, particularly for pre-mRNAs that contain cytidine-rich sequences. It can also bind poly(C) single-stranded DNA. hnRNP K plays an important role in p53/TP53 response to DNA damage, acting at the level of both transcription activation and repression. hnRNP K contains three K-homology (KH) RNA-binding domains. The model corresponds to the first one.

                        10        20        30
                ....*....|....*....|....*....|....*....
gi 5730027  159 RVLIPVKQypkfnfVGKILGPQGNTIKRLQEETGAKISV 197
Cdd:cd22432   5 RLLIPSKA------AGAIIGKGGENIKRLRTEYNASVSV 37

first type I K homology (KH) RNA-binding domain found in poly(rC)-binding protein 3 (PCBP3) and similar proteins; PCBP3, also called alpha-CP3, or PCBP3-overlapping transcript, or PCBP3-overlapping transcript 1, or heterogeneous nuclear ribonucleoprotein E3, or hnRNP E3, is a single-stranded nucleic acid binding protein that binds preferentially to oligo dC. It can function as a repressor dependent on binding to single-strand and double-stranded poly(C) sequences. PCBP3 contains three K-homology (KH) RNA-binding domains. The model corresponds to the first one.

                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*
gi 5730027  153 NMKLKERVLIPVKQypkfnfVGKILGPQGNTIKRLQEETGAKISV 197
Cdd:cd22516   6 NVTLTIRLLMHGKE------VGSIIGKKGETVKKMREESGARINI 44

first type I K homology (KH) RNA-binding domain found in Saccharomyces cerevisiae Protein SCP160 and similar proteins; SCP160, also called protein HX, is a new yeast protein associated with the nuclear membrane and the endoplasmic reticulum. It is involved in the control of mitotic chromosome transmission. It is required during cell division for faithful partitioning of the ER-nuclear envelope membranes which enclose the duplicated chromosomes in yeast. SCP160 contains seven K-homology (KH) RNA-binding domains. The model corresponds to the first one.

                        10        20
                ....*....|....*....|....*..
gi 5730027  171 NFVGKILGPQGNTIKRLQEETGAKISV 197
Cdd:cd22446  16 SVRGAIIGSRGKNLKSIQDKTGTKIQI 42

fifth type I K homology (KH) RNA-binding domain found in Arabidopsis thaliana RNA-binding KH domain-containing protein RCF3 and similar protein; RCF3, also called protein ENHANCED STRESS RESPONSE 1 (ESR1), or protein HIGH OSMOTIC STRESS GENE EXPRESSION 5 (HOS5), or protein REGULATOR OF CBF GENE EXPRESSION 3, or protein SHINY 1 (SHI1), acts as negative regulator of osmotic stress-induced gene expression. It is involved in the regulation of thermotolerance responses under heat stress. It functions as an upstream regulator of heat stress transcription factor (HSF) genes. HEN4, also called protein HUA ENHANCER 4, plays a role in floral reproductive organ identity in the third whorl and floral determinacy specification by specifically promoting the processing of AGAMOUS (AG) pre-mRNA. It functions in association with HUA1 and HUA2. RCF3 contains five K-homology (KH) RNA-binding domains. The model corresponds to the KH5 domain of RCF3.

                        10        20        30        40
                ....*....|....*....|....*....|....*....|...
gi 5730027  172 FVGKILGPQGNTIKRLQEETGAKISVlgkgsMRDKAKEEELRK 214
Cdd:cd22463  12 VVGLIIGKSGNTIKQISERSGAFVAI-----VQDRYPLEETQK 49