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SRBD1 S1 RNA binding domain 1 [ Homo sapiens (human) ]

Gene ID: 55133, updated on 27-Nov-2024

Summary

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Official Symbol
SRBD1provided by HGNC
Official Full Name
S1 RNA binding domain 1provided by HGNC
Primary source
HGNC:HGNC:25521
See related
Ensembl:ENSG00000068784 AllianceGenome:HGNC:25521
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
Summary
Predicted to enable mRNA binding activity. Predicted to be a structural constituent of ribosome. Predicted to be involved in translation. [provided by Alliance of Genome Resources, Nov 2024]
Expression
Ubiquitous expression in thyroid (RPKM 5.6), testis (RPKM 5.3) and 25 other tissues See more
Orthologs
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Genomic context

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See SRBD1 in Genome Data Viewer
Location:
2p21
Exon count:
23
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (45388680..45611267, complement)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (45393909..45616311, complement)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (45615819..45838406, complement)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105374576 Neighboring gene long intergenic non-protein coding RNA 1121 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:45446124-45447052 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:45447053-45447979 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:45483718-45484291 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:45484292-45484864 Neighboring gene uncharacterized LOC105374577 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:45570374-45571192 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:45571193-45572010 Neighboring gene Sharpr-MPRA regulatory region 15185 Neighboring gene NANOG hESC enhancer GRCh37_chr2:45693107-45693617 Neighboring gene Sharpr-MPRA regulatory region 7031 Neighboring gene RNA, 7SL, cytoplasmic 414, pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid active region 15687 Neighboring gene ReSE screen-validated silencer GRCh37_chr2:45867535-45867711 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11438 Neighboring gene uncharacterized LOC102724965 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11439 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11440 Neighboring gene Sharpr-MPRA regulatory region 4153 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:45878872-45879492 Neighboring gene ReSE screen-validated silencer GRCh37_chr2:45899906-45900117 Neighboring gene PRKCE antisense RNA 1 Neighboring gene protein kinase C epsilon

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. Lack of correlation between S1 RNA binding domain 1 SNP rs3213787/rs11884064 and normal-tension glaucoma in a population from the Republic of Korea. Jung SH, et al. Medicine (Baltimore), 2020 Jun 19. PMID 32569157, Free PMC Article
  2. Genome-wide association study of normal tension glaucoma: common variants in SRBD1 and ELOVL5 contribute to disease susceptibility. Writing Committee for the Normal Tension Glaucoma Genetic Study Group of Japan Glaucoma Society, et al. Ophthalmology, 2010 Jul. PMID 20363506
  3. Dogs and humans share a common susceptibility gene SRBD1 for glaucoma risk. Kanemaki N, et al. PLoS One, 2013. PMID 24040232, Free PMC Article
  4. Fbxl17 is rearranged in breast cancer and loss of its activity leads to increased global O-GlcNAcylation. Mason B, et al. Cell Mol Life Sci, 2020 Jul. PMID 31560077, Free PMC Article
  5. Dependence of Human Colorectal Cells Lacking the FBW7 Tumor Suppressor on the Spindle Assembly Checkpoint. Bailey ML, et al. Genetics, 2015 Nov. PMID 26354767, Free PMC Article

See all (64) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. rs3213787 and rs11884064 not associated with genetic susceptibility to normal-tension glaucoma in a Korean cohort
    Title: Lack of correlation between S1 RNA binding domain 1 SNP rs3213787/rs11884064 and normal-tension glaucoma in a population from the Republic of Korea.
  2. Dogs and humans share a common susceptibility gene SRBD1 for glaucoma risk.
    Title: Dogs and humans share a common susceptibility gene SRBD1 for glaucoma risk.
  3. Our genome-wide association study identified SRBD1 and ELOVL5 as new susceptibility genes for (normal tension glaucoma) NTG.
    Title: Genome-wide association study of normal tension glaucoma: common variants in SRBD1 and ELOVL5 contribute to disease susceptibility.
  4. Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
    Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
  5. Observational study and genome-wide association study of gene-disease association. (HuGE Navigator)
    Title: Genome-wide association study of normal tension glaucoma: common variants in SRBD1 and ELOVL5 contribute to disease susceptibility.
  6. Observational study of gene-disease association. (HuGE Navigator)
    Title: Coeliac disease-associated risk variants in TNFAIP3 and REL implicate altered NF-kappaB signalling.
Submit: New GeneRIF Correction

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

EBI GWAS Catalog

Description
Genome-wide association study of normal tension glaucoma: common variants in SRBD1 and ELOVL5 contribute to disease susceptibility.
EBI GWAS Catalog

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

HIV-1 interactions

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Protein interactions

Protein Gene Interaction Pubs
Rev rev HIV-1 Rev interacting protein, S1 RNA binding domain 1 (SRBD1), is identified by the in-vitro binding experiments involving cytosolic or nuclear extracts from HeLa cells PubMed

Go to the HIV-1, Human Interaction Database

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • FLJ10379

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables mRNA binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables structural constituent of ribosome IBA
Inferred from Biological aspect of Ancestor
more info
  
Process Evidence Code Pubs
involved_in nucleobase-containing compound metabolic process IEA
Inferred from Electronic Annotation
more info
  
involved_in translation IBA
Inferred from Biological aspect of Ancestor
more info
  

General protein information

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Preferred Names
S1 RNA-binding domain-containing protein 1
Names
H_NH0576F01.1
WUGSC:H_NH0576F01.1

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_018079.5 → NP_060549.4  S1 RNA-binding domain-containing protein 1

    See identical proteins and their annotated locations for NP_060549.4

    Status: VALIDATED

    Source sequence(s)
    AK056536, BC032538, DA235970
    Consensus CDS
    CCDS1823.1
    UniProtKB/Swiss-Prot
    Q53T56, Q8N5C6, Q96TA4, Q9NW11
    UniProtKB/TrEMBL
    B3KPM8
    Related
    ENSP00000263736.4, ENST00000263736.5
    Conserved Domains (5) summary
    COG2183
    Location:208 → 991
    Tex; Transcriptional accessory protein Tex/SPT6 [Transcription]
    cd05685
    Location:919 → 990
    S1_Tex; S1_Tex: The C-terminal S1 domain of a transcription accessory factor called Tex, which has been characterized in Bordetella pertussis and Pseudomonas aeruginosa. The tex gene is essential in Bortella pertusis and is named for its role in toxin expression. ...
    pfam09371
    Location:219 → 414
    Tex_N; Tex-like protein N-terminal domain
    pfam12836
    Location:705 → 767
    HHH_3; Helix-hairpin-helix motif
    pfam16921
    Location:538 → 663
    Tex_YqgF; Tex protein YqgF-like domain

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000002.12 Reference GRCh38.p14 Primary Assembly

    Range
    45388680..45611267 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011532946.3 → XP_011531248.1  S1 RNA-binding domain-containing protein 1 isoform X1

    UniProtKB/TrEMBL
    B3KPM8
    Conserved Domains (5) summary
    COG2183
    Location:208 → 975
    Tex; Transcriptional accessory protein Tex/SPT6 [Transcription]
    cd05685
    Location:903 → 974
    S1_Tex; S1_Tex: The C-terminal S1 domain of a transcription accessory factor called Tex, which has been characterized in Bordetella pertussis and Pseudomonas aeruginosa. The tex gene is essential in Bortella pertusis and is named for its role in toxin expression. ...
    pfam09371
    Location:219 → 414
    Tex_N; Tex-like protein N-terminal domain
    pfam12836
    Location:689 → 751
    HHH_3; Helix-hairpin-helix motif
    cl21482
    Location:538 → 647
    RuvC_resolvase; Holliday junction resolvases (HJRs) are endonucleases that specifically resolve Holliday junction DNA intermediates during homologous recombination. HJR's occur in archaea, bacteria, and in the mitochondria of certain fungi, however this CD includes ...

  2. XM_047444862.1 → XP_047300818.1  S1 RNA-binding domain-containing protein 1 isoform X5

    UniProtKB/TrEMBL
    B7Z6X7

  3. XM_047444861.1 → XP_047300817.1  S1 RNA-binding domain-containing protein 1 isoform X5

    UniProtKB/TrEMBL
    B7Z6X7

  4. XM_047444860.1 → XP_047300816.1  S1 RNA-binding domain-containing protein 1 isoform X4

  5. XM_047444858.1 → XP_047300814.1  S1 RNA-binding domain-containing protein 1 isoform X2

  6. XM_047444859.1 → XP_047300815.1  S1 RNA-binding domain-containing protein 1 isoform X3

  7. XM_047444857.1 → XP_047300813.1  S1 RNA-binding domain-containing protein 1 isoform X2

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060926.1 Alternate T2T-CHM13v2.0

    Range
    45393909..45616311 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054342728.1 → XP_054198703.1  S1 RNA-binding domain-containing protein 1 isoform X1

  2. XM_054342734.1 → XP_054198709.1  S1 RNA-binding domain-containing protein 1 isoform X5

    UniProtKB/TrEMBL
    B7Z6X7

  3. XM_054342735.1 → XP_054198710.1  S1 RNA-binding domain-containing protein 1 isoform X6

  4. XM_054342733.1 → XP_054198708.1  S1 RNA-binding domain-containing protein 1 isoform X5

    UniProtKB/TrEMBL
    B7Z6X7

  5. XM_054342732.1 → XP_054198707.1  S1 RNA-binding domain-containing protein 1 isoform X4

  6. XM_054342730.1 → XP_054198705.1  S1 RNA-binding domain-containing protein 1 isoform X2

  7. XM_054342731.1 → XP_054198706.1  S1 RNA-binding domain-containing protein 1 isoform X3

  8. XM_054342729.1 → XP_054198704.1  S1 RNA-binding domain-containing protein 1 isoform X2

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q8N5C6.2 GenPept UniProtKB/Swiss-Prot:Q8N5C6

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