U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

Links from GEO Profiles

    • Showing Current items.

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

    Gene ID: 55133, updated on 2-Nov-2024

    Summary

    Go to the top of the page Help
    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
    mouse all
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    Go to the top of the page Help
    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

    Go to the top of the page Help

    Go to nucleotide: Graphics FASTA GenBank

    Expression

    Go to the top of the page Help
    • Project title: HPA RNA-seq normal tissues 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

    Go to the top of the pageHelp

    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 (61) 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

    Go to the top of the page Help

    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

    Go to the top of the page Help

    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Genotypes

    HIV-1 interactions

    Go to the top of the page Help

    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

    Go to the top of the page Help
    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Go to the top of the page Help

    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

    Go to the top of the page Help
    Preferred Names
    S1 RNA-binding domain-containing protein 1
    Names
    H_NH0576F01.1
    WUGSC:H_NH0576F01.1

    NCBI Reference Sequences (RefSeq)

    Go to the top of the page Help

    NEW Try the new Transcript table

    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

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

    Chemical Information
    Molecular Biology Databases
    Research Materials
    Tools