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

Gene ID: 148418, updated on 5-Aug-2022

Summary

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

See SAMD13 in Genome Data Viewer
Location:
1p31.1
Exon count:
6
Annotation release Status Assembly Chr Location
110 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (84298538..84350798)
110 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 small nucleolar RNA SNORA2/SNORA34 family Neighboring gene urate oxidase (pseudogene) Neighboring gene Sharpr-MPRA regulatory region 5400 Neighboring gene deoxyribonuclease 2 beta

Genomic regions, transcripts, and products

Expression

  • 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

Phenotypes

EBI GWAS Catalog

Description
Novel genetic loci identified for the pathophysiology of childhood obesity in the Hispanic population.
EBI GWAS Catalog

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables chromatin binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
enables histone binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
Process Evidence Code Pubs
involved_in negative regulation of DNA-templated transcription IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
Component Evidence Code Pubs
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 

General protein information

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_001010971.3NP_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:42110
    SAM_Atherin-like; SAM domain of Atherin/Atherin-like subfamily
  2. NM_001134663.2NP_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:2896
    SAM_Atherin-like; SAM domain of Atherin/Atherin-like subfamily
  3. NM_001134664.2NP_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:2896
    SAM_Atherin-like; SAM domain of Atherin/Atherin-like subfamily

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 110 details...Open this link in a new tab

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_017000377.3XP_016855866.1  sterile alpha motif domain-containing protein 13 isoform X1

    UniProtKB/Swiss-Prot
    Q5VXD3, Q5VXD4
    Related
    ENSP00000359705.3, ENST00000370671.7
    Conserved Domains (2) summary
    cd09583
    Location:48116
    SAM_Atherin-like; SAM domain of Atherin/Atherin-like subfamily
    smart00454
    Location:48104
    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)