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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
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Genomic context

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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

Gene LinkOut

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