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

Gene ID: 148418, updated on 5-Mar-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 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
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
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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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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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