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    YJU2B YJU2 splicing factor homolog B [ Homo sapiens (human) ]

    Gene ID: 81576, updated on 3-Apr-2024

    Summary

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    Official Symbol
    YJU2Bprovided by HGNC
    Official Full Name
    YJU2 splicing factor homolog Bprovided by HGNC
    Primary source
    HGNC:HGNC:28118
    See related
    Ensembl:ENSG00000104957 AllianceGenome:HGNC:28118
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    CCDC130
    Summary
    Involved in response to virus. Predicted to be part of U2-type spliceosomal complex and post-mRNA release spliceosomal complex. [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Ubiquitous expression in spleen (RPKM 12.4), endometrium (RPKM 9.8) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See YJU2B in Genome Data Viewer
    Location:
    19p13.13
    Exon count:
    12
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 19 NC_000019.10 (13731752..13763289)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (13857964..13889514)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (13842566..13874103)

    Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC107985287 Neighboring gene ReSE screen-validated silencer GRCh37_chr19:13700158-13700387 Neighboring gene Sharpr-MPRA regulatory region 13460 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr19:13732208-13732929 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:13776728-13777228 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:13777229-13777729 Neighboring gene uncharacterized LOC105372284 Neighboring gene MPRA-validated peak3373 silencer Neighboring gene MPRA-validated peak3374 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14133 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10207 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:13873547-13874063 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10208 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:13876533-13877162 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14134 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14135 Neighboring gene H3K27ac hESC enhancer GRCh37_chr19:13885277-13885806 Neighboring gene H3K27ac hESC enhancer GRCh37_chr19:13885807-13886335 Neighboring gene chromosome 19 open reading frame 53 Neighboring gene methylthioribose-1-phosphate isomerase 1

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

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    Related articles in PubMed

    1. Alternative mechanisms for gene activation induced by poly(rI).poly(rC) and Newcastle disease virus. Lammers R, et al. Eur J Biochem, 1988 Dec 1. PMID 3203696
    2. Dynamic protein-protein interaction wiring of the human spliceosome. Hegele A, et al. Mol Cell, 2012 Feb 24. PMID 22365833
    3. DCAF8, a novel MuRF1 interaction partner, promotes muscle atrophy. Nowak M, et al. J Cell Sci, 2019 Sep 6. PMID 31391242
    4. Mutual regulation between OGT and XIAP to control colon cancer cell growth and invasion. Seo HG, et al. Cell Death Dis, 2020 Sep 29. PMID 32994395, Free PMC Article
    5. Competitive binding of E3 ligases TRIM26 and WWP2 controls SOX2 in glioblastoma. Mahlokozera T, et al. Nat Commun, 2021 Nov 3. PMID 34732716, Free PMC Article

    See all (20) citations in PubMed

    GeneRIFs: Gene References Into Functions

    Phenotypes

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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Genotypes

    Pathways from PubChem

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    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • MGC10471

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in RNA splicing IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in mRNA splicing, via spliceosome IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in response to virus IEP
    Inferred from Expression Pattern
    more info
    		 PubMed 
    Component Evidence Code Pubs
    part_of U2-type spliceosomal complex IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    is_active_in cellular_component ND
    No biological Data available
    more info
    		  
    part_of post-mRNA release spliceosomal complex IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    probable splicing factor YJU2B
    Names
    9 kDa protein
    coiled-coil domain containing 130
    coiled-coil domain-containing protein 130

    NCBI Reference Sequences (RefSeq)

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    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    mRNA and Protein(s)

    1. NM_001320561.2 → NP_001307490.1  probable splicing factor YJU2B isoform a

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) differs in the 5' UTR compared to variant 1. Variants 1, 2, 3, and 4 all encode the same isoform (a).
      Source sequence(s)
      AC008686, AK293927, BC002905, HY078789
      Consensus CDS
      CCDS12296.1
      UniProtKB/Swiss-Prot
      P13994, Q9BQ72
      UniProtKB/TrEMBL
      B3KUZ1
      Conserved Domains (1) summary
      pfam04502
      Location:8 → 221
      DUF572; Family of unknown function (DUF572)

    2. NM_001320564.2 → NP_001307493.1  probable splicing factor YJU2B isoform a

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) differs in the 5' UTR compared to variant 1. Variants 1, 2, 3, and 4 all encode the same isoform (a).
      Source sequence(s)
      AC008686, AK293927, BC002905, BX394050
      Consensus CDS
      CCDS12296.1
      UniProtKB/Swiss-Prot
      P13994, Q9BQ72
      UniProtKB/TrEMBL
      B3KUZ1
      Conserved Domains (1) summary
      pfam04502
      Location:8 → 221
      DUF572; Family of unknown function (DUF572)

    3. NM_001320565.2 → NP_001307494.1  probable splicing factor YJU2B isoform a

      Status: VALIDATED

      Description
      Transcript Variant: This variant (4) differs in the 5' UTR compared to variant 1. Variants 1, 2, 3, and 4 all encode the same isoform (a).
      Source sequence(s)
      AC008686, AL560878, BC002905
      Consensus CDS
      CCDS12296.1
      UniProtKB/Swiss-Prot
      P13994, Q9BQ72
      UniProtKB/TrEMBL
      B3KUZ1
      Related
      ENSP00000465776.1, ENST00000586600.5
      Conserved Domains (1) summary
      pfam04502
      Location:8 → 221
      DUF572; Family of unknown function (DUF572)

    4. NM_001320566.2 → NP_001307495.1  probable splicing factor YJU2B isoform b

      Status: VALIDATED

      Description
      Transcript Variant: This variant (5) differs in the 5' UTR and coding sequence and retains an intron compared to variant 1. The resulting isoform (b) is shorter at the N-terminus compared to isoform a. Variants 5, 6, and 7 all encode the same isoform (b).
      Source sequence(s)
      AC008686, AK293927, BC002905, BX394050
      UniProtKB/Swiss-Prot
      P13994
      UniProtKB/TrEMBL
      B7Z1U2
      Conserved Domains (1) summary
      pfam04502
      Location:1 → 93
      DUF572; Family of unknown function (DUF572)

    5. NM_001320567.2 → NP_001307496.1  probable splicing factor YJU2B isoform b

      Status: VALIDATED

      Description
      Transcript Variant: This variant (6) differs in the 5' UTR and coding sequence and retains an intron compared to variant 1. The resulting isoform (b) is shorter at the N-terminus compared to isoform a. Variants 5, 6, and 7 all encode the same isoform (b).
      Source sequence(s)
      AC008686, AK293927, BC002905, KC877714
      UniProtKB/Swiss-Prot
      P13994
      UniProtKB/TrEMBL
      B7Z1U2
      Conserved Domains (1) summary
      pfam04502
      Location:1 → 93
      DUF572; Family of unknown function (DUF572)

    6. NM_001320568.2 → NP_001307497.1  probable splicing factor YJU2B isoform b

      Status: VALIDATED

      Description
      Transcript Variant: This variant (7) retains an intron compared to variant 1. The resulting isoform (b) is shorter at the N-terminus compared to isoform a. Variants 5, 6, and 7 all encode the same isoform (b).
      Source sequence(s)
      BC002905, BM547551, CR999732
      UniProtKB/Swiss-Prot
      P13994
      Related
      ENST00000593174.5
      Conserved Domains (1) summary
      pfam04502
      Location:1 → 93
      DUF572; Family of unknown function (DUF572)

    7. NM_001320569.2 → NP_001307498.1  probable splicing factor YJU2B isoform c

      Status: VALIDATED

      Description
      Transcript Variant: This variant (8) lacks an alternate exon compared to variant 1. The resulting isoform (c) is shorter at the N-terminus compared to isoform a.
      Source sequence(s)
      AC008686, BC002905, BI913255, BX422326
      UniProtKB/TrEMBL
      B3KUZ1
      Conserved Domains (3) summary
      PHA03193
      Location:199 → 337
      PHA03193; tegument protein VP11/12; Provisional
      COG5134
      Location:1 → 182
      COG5134; Uncharacterized conserved protein [Function unknown]
      pfam04502
      Location:1 → 189
      DUF572; Family of unknown function (DUF572)

    8. NM_030818.4 → NP_110445.1  probable splicing factor YJU2B isoform a

      See identical proteins and their annotated locations for NP_110445.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) encodes the longest isoform (a). Variants 1, 2, 3, and 4 all encode the same isoform (a).
      Source sequence(s)
      BC002905, BM547551
      Consensus CDS
      CCDS12296.1
      UniProtKB/Swiss-Prot
      P13994, Q9BQ72
      UniProtKB/TrEMBL
      B3KUZ1
      Related
      ENSP00000221554.7, ENST00000221554.13
      Conserved Domains (1) summary
      pfam04502
      Location:8 → 221
      DUF572; Family of unknown function (DUF572)

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000019.10 Reference GRCh38.p14 Primary Assembly

      Range
      13731752..13763289
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_005260086.5 → XP_005260143.1  probable splicing factor YJU2B isoform X1

      See identical proteins and their annotated locations for XP_005260143.1

      UniProtKB/Swiss-Prot
      P13994, Q9BQ72
      UniProtKB/TrEMBL
      B3KUZ1
      Conserved Domains (1) summary
      pfam04502
      Location:8 → 221
      DUF572; Family of unknown function (DUF572)

    2. XM_047439475.1 → XP_047295431.1  probable splicing factor YJU2B isoform X2

    3. XM_011528326.3 → XP_011526628.1  probable splicing factor YJU2B isoform X2

      See identical proteins and their annotated locations for XP_011526628.1

      Conserved Domains (1) summary
      cl40657
      Location:7 → 146
      DUF572; Family of unknown function (DUF572)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060943.1 Alternate T2T-CHM13v2.0

      Range
      13857964..13889514
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054322246.1 → XP_054178221.1  probable splicing factor YJU2B isoform X1

      UniProtKB/Swiss-Prot
      P13994, Q9BQ72

    2. XM_054322247.1 → XP_054178222.1  probable splicing factor YJU2B isoform X2

    3. XM_054322248.1 → XP_054178223.1  probable splicing factor YJU2B isoform X2

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    P13994.2 GenPept UniProtKB/Swiss-Prot:P13994

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