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    SAMD13 sterile alpha motif domain containing 13 [ Homo sapiens (human) ]

    Gene ID: 148418, updated on 28-Apr-2024

    Summary

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    Official Symbol
    SAMD13provided by HGNC
    Official Full Name
    sterile alpha motif domain containing 13provided by HGNC
    Primary source
    HGNC:HGNC:24582
    See related
    Ensembl:ENSG00000203943 MIM:620800; AllianceGenome:HGNC:24582
    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
    DJL; HSD-41; HSD-42
    Summary
    Predicted to enable chromatin binding activity and histone binding activity. Predicted to be involved in negative regulation of transcription, DNA-templated. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Broad expression in colon (RPKM 4.2), testis (RPKM 3.9) and 16 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See SAMD13 in Genome Data Viewer
    Location:
    1p31.1
    Exon count:
    6
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (84298538..84350798)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (84139002..84191273)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (84764221..84816481)

    Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene Sharpr-MPRA regulatory region 3408 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr1:84720292-84720890 Neighboring gene NEDD8 pseudogene 1 Neighboring gene NANOG hESC enhancer GRCh37_chr1:84724969-84725470 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1248 Neighboring gene small nucleolar RNA SNORA2/SNORA34 family Neighboring gene MPRA-validated peak299 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1018 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr1:84830842-84832041 Neighboring gene urate oxidase (pseudogene) Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1249 Neighboring gene Sharpr-MPRA regulatory region 5400 Neighboring gene deoxyribonuclease 2 beta

    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. A High-Density Map for Navigating the Human Polycomb Complexome. Hauri S, et al. Cell Rep, 2016 Oct 4. PMID 27705803
    2. Novel genetic loci identified for the pathophysiology of childhood obesity in the Hispanic population. Comuzzie AG, et al. PLoS One, 2012. PMID 23251661, Free PMC Article
    3. The DNA sequence and biological annotation of human chromosome 1. Gregory SG, et al. Nature, 2006 May 18. PMID 16710414
    4. Genome-wide CRISPR screen identifies HNRNPL as a prostate cancer dependency regulating RNA splicing. Fei T, et al. Proc Natl Acad Sci U S A, 2017 Jun 27. PMID 28611215, Free PMC Article
    5. Human-chromatin-related protein interactions identify a demethylase complex required for chromosome segregation. Marcon E, et al. Cell Rep, 2014 Jul 10. PMID 24981860

    See all (10) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. SAMD13 serves as a useful prognostic biomarker for hepatocellular carcinoma.
      Title: SAMD13 serves as a useful prognostic biomarker for hepatocellular carcinoma.
    Submit: New GeneRIF Correction

    Phenotypes

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    Review eQTL and phenotype association data in this region using PheGenI

    EBI GWAS Catalog

    Description
    Novel genetic loci identified for the pathophysiology of childhood obesity in the Hispanic 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

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    General protein information

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    Preferred Names
    sterile alpha motif domain-containing protein 13
    Names
    SAM domain-containing protein 13
    dnaj-like protein (LOC148418)

    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_001010971.3 → NP_001010971.1  sterile alpha motif domain-containing protein 13 isoform 1

      See identical proteins and their annotated locations for NP_001010971.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and it encodes the longer protein (isoform 1).
      Source sequence(s)
      AL359273
      Consensus CDS
      CCDS30760.1
      UniProtKB/Swiss-Prot
      Q5VXD3
      Related
      ENSP00000359707.3, ENST00000370673.7
      Conserved Domains (1) summary
      cd09583
      Location:42 → 110
      SAM_Atherin-like; SAM domain of Atherin/Atherin-like subfamily

    2. NM_001134663.2 → NP_001128135.1  sterile alpha motif domain-containing protein 13 isoform 2

      See identical proteins and their annotated locations for NP_001128135.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) has multiple differences in the 5' UTR and 5' coding region, which results in the use of a downstream AUG start codon, compared to variant 1. Variants 2 and 3 both encode the same protein (isoform 2).
      Source sequence(s)
      AL359273
      Consensus CDS
      CCDS44166.1
      UniProtKB/Swiss-Prot
      Q5VXD3
      Related
      ENSP00000378311.3, ENST00000394834.8
      Conserved Domains (1) summary
      cd09583
      Location:28 → 96
      SAM_Atherin-like; SAM domain of Atherin/Atherin-like subfamily

    3. NM_001134664.2 → NP_001128136.1  sterile alpha motif domain-containing protein 13 isoform 2

      See identical proteins and their annotated locations for NP_001128136.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) has multiple differences in the 5' UTR and 5' coding region, which results in the use of a downstream AUG start codon, compared to variant 1. Variants 2 and 3 both encode the same protein (isoform 2).
      Source sequence(s)
      AL359273
      Consensus CDS
      CCDS44166.1
      UniProtKB/Swiss-Prot
      Q5VXD3
      Related
      ENSP00000359702.3, ENST00000370668.7
      Conserved Domains (1) summary
      cd09583
      Location:28 → 96
      SAM_Atherin-like; SAM domain of Atherin/Atherin-like subfamily

    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_000001.11 Reference GRCh38.p14 Primary Assembly

      Range
      84298538..84350798
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_017000377.3 → XP_016855866.1  sterile alpha motif domain-containing protein 13 isoform X1

      UniProtKB/Swiss-Prot
      B3KPW8, D3DT11, Q53AI4, Q5VXD2, Q5VXD3, Q5VXD4
      Related
      ENSP00000359705.3, ENST00000370671.7
      Conserved Domains (2) summary
      cd09583
      Location:48 → 116
      SAM_Atherin-like; SAM domain of Atherin/Atherin-like subfamily
      smart00454
      Location:48 → 104
      SAM; Sterile alpha motif

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060925.1 Alternate T2T-CHM13v2.0

      Range
      84139002..84191273
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054334573.1 → XP_054190548.1  sterile alpha motif domain-containing protein 13 isoform X1

      UniProtKB/Swiss-Prot
      B3KPW8, D3DT11, Q53AI4, Q5VXD2, Q5VXD3, Q5VXD4
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q5VXD3.1 GenPept UniProtKB/Swiss-Prot:Q5VXD3

    Gene LinkOut

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

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