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    TSBP1 testis expressed basic protein 1 [ Homo sapiens (human) ]

    Gene ID: 10665, updated on 3-Nov-2024

    Summary

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    Official Symbol
    TSBP1provided by HGNC
    Official Full Name
    testis expressed basic protein 1provided by HGNC
    Primary source
    HGNC:HGNC:13922
    See related
    Ensembl:ENSG00000204296 MIM:618151; AllianceGenome:HGNC:13922
    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
    TSBP; C6orf10
    Summary
    Located in nucleus. [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Restricted expression toward testis (RPKM 6.6) See more
    Orthologs
    mouse all
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    Genomic context

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    See TSBP1 in Genome Data Viewer
    Location:
    6p21.32
    Exon count:
    29
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (32292698..32371903, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (32145999..32224841, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (32260475..32339680, complement)

    Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:32156057-32156613 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:32157766-32158334 Neighboring gene ReSE screen-validated silencer GRCh37_chr6:32158721-32158899 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:32163365-32164145 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:32164146-32164927 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:32164928-32165708 Neighboring gene PBX homeobox 2 Neighboring gene G protein signaling modulator 3 Neighboring gene notch receptor 4 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:32222789-32223446 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:32223447-32224103 Neighboring gene TSBP1 and BTNL2 antisense RNA 1 Neighboring gene MPRA-validated peak5754 silencer Neighboring gene heterogeneous nuclear ribonucleoprotein A1 pseudogene 2 Neighboring gene MPRA-validated peak5755 silencer Neighboring gene RNA, U6 small nuclear 603, pseudogene Neighboring gene ReSE screen-validated silencer GRCh37_chr6:32382003-32382278 Neighboring gene ReSE screen-validated silencer GRCh37_chr6:32382475-32382623 Neighboring gene HLA complex group 23 Neighboring gene butyrophilin like 2 Neighboring gene major histocompatibility complex, class II, DR alpha

    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 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. Impact of missense TSBP1 variants on the susceptibility to coronary heart disease. Yang W, et al. Gene, 2024 Feb 20. PMID 38042215
    2. A genome-wide association study in progressive multiple sclerosis. Martinelli-Boneschi F, et al. Mult Scler, 2012 Oct. PMID 22457343
    3. Genome-wide analysis identifies a quantitative trait locus in the MHC class II region associated with generalized vitiligo age of onset. Jin Y, et al. J Invest Dermatol, 2011 Jun. PMID 21326295, Free PMC Article
    4. Identification of a novel risk locus for multiple sclerosis at 13q31.3 by a pooled genome-wide scan of 500,000 single nucleotide polymorphisms. Comabella M, et al. PLoS One, 2008. PMID 18941528, Free PMC Article
    5. Multilocus evaluation of genetic predictors of multiple sclerosis. Timasheva Y, et al. Gene, 2022 Jan 30. PMID 34656742

    See all (50) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Impact of missense TSBP1 variants on the susceptibility to coronary heart disease.
      Title: Impact of missense TSBP1 variants on the susceptibility to coronary heart disease.
    2. Multilocus evaluation of genetic predictors of multiple sclerosis.
      Title: Multilocus evaluation of genetic predictors of multiple sclerosis.
    3. Shared Signature of Recent Positive Selection on the TSBP1-BTNL2-HLA-DRA Genes in Five Native Populations from North Borneo.
      Title: Shared Signature of Recent Positive Selection on the TSBP1-BTNL2-HLA-DRA Genes in Five Native Populations from North Borneo.
    4. Our findings suggest that CpG-single nucleotide polymorphisms at the C6orf10/LOC101929163 locus might modify age of onset in C9orf72 carriers belonging to the entire amyotrophic lateral sclerosis-frontotemporal dementia spectrum by controlling DNA methylation and gene expression
      Title: A C6orf10/LOC101929163 locus is associated with age of onset in C9orf72 carriers.
    5. Observational study and genome-wide association study of gene-disease association, gene-environment interaction, and pharmacogenomic / toxicogenomic. (HuGE Navigator)
      Title: A genome-wide study identifies HLA alleles associated with lumiracoxib-related liver injury.
    6. Observational study and genome-wide association study of gene-disease association. (HuGE Navigator)
      Title: Identification of candidate loci at 6p21 and 21q22 in a genome-wide association study of cardiac manifestations of neonatal lupus.
    7. Observational study of gene-disease association and gene-gene interaction. (HuGE Navigator)
      Title: Association of MHC SNP genotype with susceptibility to type 1 diabetes: a modified survival approach.
    8. Observational study of gene-disease association. (HuGE Navigator)
      Title: Examination of genetic polymorphisms in newborns for signatures of sex-specific prenatal selection.
    Submit: New GeneRIF Correction

    Phenotypes

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    Review eQTL and phenotype association data in this region using PheGenI

    EBI GWAS Catalog

    Description
    A genome-wide association study identifies multiple susceptibility loci for chronic lymphocytic leukemia.
    EBI GWAS Catalog
    A genome-wide association study identifies polymorphisms in the HLA-DR region associated with non-response to hepatitis B vaccination in Chinese Han populations.
    EBI GWAS Catalog
    A genome-wide association study in progressive multiple sclerosis.
    EBI GWAS Catalog
    A genome-wide association study of HCV-induced liver cirrhosis in the Japanese population identifies novel susceptibility loci at the MHC region.
    EBI GWAS Catalog
    A genome-wide association study reveals ARL15, a novel non-HLA susceptibility gene for rheumatoid arthritis in North Indians.
    EBI GWAS Catalog
    A genome-wide study identifies HLA alleles associated with lumiracoxib-related liver injury.
    EBI GWAS Catalog
    Association of the TRAF1-C5 locus on chromosome 9 with juvenile idiopathic arthritis.
    EBI GWAS Catalog
    Differential genetic associations for systemic lupus erythematosus based on anti-dsDNA autoantibody production.
    EBI GWAS Catalog
    Genetic associations for activated partial thromboplastin time and prothrombin time, their gene expression profiles, and risk of coronary artery disease.
    EBI GWAS Catalog
    Genetics of coronary artery calcification among African Americans, a meta-analysis.
    EBI GWAS Catalog
    Genome-wide analysis identifies a quantitative trait locus in the MHC class II region associated with generalized vitiligo age of onset.
    EBI GWAS Catalog
    Genome-wide association for abdominal subcutaneous and visceral adipose reveals a novel locus for visceral fat in women.
    EBI GWAS Catalog
    Genome-wide association study identifies eight new susceptibility loci for atopic dermatitis in the Japanese population.
    EBI GWAS Catalog
    Genome-wide association study identifies three new susceptibility loci for adult asthma in the Japanese population.
    EBI GWAS Catalog
    Genome-wide association study in Han Chinese identifies four new susceptibility loci for coronary artery disease.
    EBI GWAS Catalog
    Genome-wide association study meta-analysis identifies seven new rheumatoid arthritis risk loci.
    EBI GWAS Catalog
    HLA has strongest association with IgA nephropathy in genome-wide analysis.
    EBI GWAS Catalog
    Identification of 23 new prostate cancer susceptibility loci using the iCOGS custom genotyping array.
    EBI GWAS Catalog
    Identification of a novel risk locus for multiple sclerosis at 13q31.3 by a pooled genome-wide scan of 500,000 single nucleotide polymorphisms.
    EBI GWAS Catalog
    Identification of independent risk loci for Graves' disease within the MHC in the Japanese population.
    EBI GWAS Catalog
    Identification of novel genetic markers associated with clinical phenotypes of systemic sclerosis through a genome-wide association strategy.
    EBI GWAS Catalog
    Lupus nephritis susceptibility Loci in women with systemic lupus erythematosus.
    EBI GWAS Catalog
    Multiple genetic loci for bone mineral density and fractures.
    EBI GWAS Catalog
    Novel genetic loci identified for the pathophysiology of childhood obesity in the Hispanic population.
    EBI GWAS Catalog
    Primary biliary cirrhosis associated with HLA, IL12A, and IL12RB2 variants.
    EBI GWAS Catalog
    Risk HLA-DQA1 and PLA(2)R1 alleles in idiopathic membranous nephropathy.
    EBI GWAS Catalog
    The human AIRE gene at chromosome 21q22 is a genetic determinant for the predisposition to rheumatoid arthritis in Japanese population.
    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)

    Genotypes

    HIV-1 interactions

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    Replication interactions

    Interaction Pubs
    Knockdown of chromosome 6 open reading frame 10 (C6orf10; TSBP) by shRNA library screening inhibits HIV-1 replication in cultured Jurkat T-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

    Gene Ontology Provided by GOA

    Component Evidence Code Pubs
    located_in membrane IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in nucleus HDA PubMed 

    General protein information

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    Preferred Names
    testis-expressed basic protein 1
    Names
    testis specific basic protein
    uncharacterized protein C6orf10

    NCBI Reference Sequences (RefSeq)

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    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_001286474.2 → NP_001273403.1  testis-expressed basic protein 1 isoform b

      See identical proteins and their annotated locations for NP_001273403.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) uses an alternate in-frame splice site and includes an additional in-frame exon in the 5' coding region, and also includes two additional in-frame exons in the central coding region, compared to variant 1. The encoded isoform (b) is shorter than isoform a.
      Source sequence(s)
      AK225742, AK310230, BC034774, BX113229, U60665
      Consensus CDS
      CCDS69082.1
      UniProtKB/TrEMBL
      A0A1U9X7D1, A0A1U9X7D7
      Related
      ENSP00000431199.1, ENST00000533191.6
      Conserved Domains (1) summary
      cl26511
      Location:219 → 561
      Neuromodulin_N; Gap junction protein N-terminal region

    2. NM_001286475.2 → NP_001273404.1  testis-expressed basic protein 1 isoform c

      See identical proteins and their annotated locations for NP_001273404.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) uses an alternate in-frame splice site and lacks an in-frame exon but includes a different in-frame exon in the 5' coding region, and also includes an additional in-frame exon in the central coding region, compared to variant 1. The encoded isoform (c) is shorter than isoform a.
      Source sequence(s)
      AK302176, BC034774, BX113229, DC399589, U60665
      Consensus CDS
      CCDS75430.1
      UniProtKB/TrEMBL
      B4DXY0, E9PLW3
      Related
      ENSP00000435103.1, ENST00000527965.5
      Conserved Domains (2) summary
      PTZ00121
      Location:205 → 547
      PTZ00121; MAEBL; Provisional
      pfam15782
      Location:62 → 223
      GREB1; Gene regulated by oestrogen in breast cancer

    3. NM_006781.5 → NP_006772.3  testis-expressed basic protein 1 isoform a

      See identical proteins and their annotated locations for NP_006772.3

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (a).
      Source sequence(s)
      AK225742, BC034774, BX113229, DC399589, U60665
      Consensus CDS
      CCDS34422.1
      UniProtKB/Swiss-Prot
      A2BET1, A2BET2, A6NME2, B0S7R2, B0S7R3, E9PMB1, Q5SPI9, Q5SPJ0, Q5SPK9, Q5SPL0, Q5SRN2, Q5SRN3, Q5TG25, Q5TG26, Q8N4B6
      UniProtKB/TrEMBL
      F8VVU2
      Related
      ENSP00000415517.2, ENST00000447241.6
      Conserved Domains (1) summary
      PTZ00121
      Location:221 → 563
      PTZ00121; MAEBL; Provisional

    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_000006.12 Reference GRCh38.p14 Primary Assembly

      Range
      32292698..32371903 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_024446307.2 → XP_024302075.1  testis-expressed basic protein 1 isoform X2

      UniProtKB/TrEMBL
      F8VVU2
      Conserved Domains (1) summary
      PTZ00121
      Location:265 → 607
      PTZ00121; MAEBL; Provisional

    2. XM_017010182.2 → XP_016865671.1  testis-expressed basic protein 1 isoform X1

      Conserved Domains (1) summary
      PTZ00121
      Location:127 → 469
      PTZ00121; MAEBL; Provisional

    Reference GRCh38.p14 ALT_REF_LOCI_1

    Genomic

    1. NT_167244.2 Reference GRCh38.p14 ALT_REF_LOCI_1

      Range
      3655064..3704149 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Reference GRCh38.p14 ALT_REF_LOCI_2

    Genomic

    1. NT_113891.3 Reference GRCh38.p14 ALT_REF_LOCI_2

      Range
      3731147..3810034 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054329723.1 → XP_054185698.1  testis-expressed basic protein 1 isoform X2

    Reference GRCh38.p14 ALT_REF_LOCI_3

    Genomic

    1. NT_167245.2 Reference GRCh38.p14 ALT_REF_LOCI_3

      Range
      3534137..3613017 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054330220.1 → XP_054186195.1  testis-expressed basic protein 1 isoform X2

    2. XM_054330219.1 → XP_054186194.1  testis-expressed basic protein 1 isoform X1

    Reference GRCh38.p14 ALT_REF_LOCI_4

    Genomic

    1. NT_167246.2 Reference GRCh38.p14 ALT_REF_LOCI_4

      Range
      3597690..3676899 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054330510.1 → XP_054186485.1  testis-expressed basic protein 1 isoform X2

    2. XM_054330509.1 → XP_054186484.1  testis-expressed basic protein 1 isoform X1

    Reference GRCh38.p14 ALT_REF_LOCI_5

    Genomic

    1. NT_167247.2 Reference GRCh38.p14 ALT_REF_LOCI_5

      Range
      3664573..3713680 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Reference GRCh38.p14 ALT_REF_LOCI_6

    Genomic

    1. NT_167248.2 Reference GRCh38.p14 ALT_REF_LOCI_6

      Range
      3516097..3594952 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054330992.1 → XP_054186967.1  testis-expressed basic protein 1 isoform X2

    2. XM_054330991.1 → XP_054186966.1  testis-expressed basic protein 1 isoform X1

    Reference GRCh38.p14 ALT_REF_LOCI_7

    Genomic

    1. NT_167249.2 Reference GRCh38.p14 ALT_REF_LOCI_7

      Range
      3608972..3687852 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054331274.1 → XP_054187249.1  testis-expressed basic protein 1 isoform X3

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060930.1 Alternate T2T-CHM13v2.0

      Range
      32145999..32224841 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054354046.1 → XP_054210021.1  testis-expressed basic protein 1 isoform X5

    2. XM_054354045.1 → XP_054210020.1  testis-expressed basic protein 1 isoform X4

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q5SRN2.3 GenPept UniProtKB/Swiss-Prot:Q5SRN2

    Gene LinkOut

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

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