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SAMD5 sterile alpha motif domain containing 5 [ Homo sapiens (human) ]

Gene ID: 389432, updated on 5-Mar-2024

Summary

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Official Symbol
SAMD5provided by HGNC
Official Full Name
sterile alpha motif domain containing 5provided by HGNC
Primary source
HGNC:HGNC:21180
See related
Ensembl:ENSG00000203727 MIM:620517; AllianceGenome:HGNC:21180
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
dJ875H10.1
Summary
Located in cytoplasm. [provided by Alliance of Genome Resources, Apr 2022]
Expression
Broad expression in placenta (RPKM 5.1), colon (RPKM 4.2) and 21 other tissues See more
Orthologs
mouse all
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Genomic context

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Location:
6q24.3
Exon count:
3
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (147508690..147954680)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (148701984..149150652)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (147829826..147891157)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124901421 Neighboring gene uncharacterized LOC105378043 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:147759841-147760442 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:147760443-147761044 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr6:147769071-147769837 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr6:147824689-147825218 Neighboring gene YAP1 pseudogene 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17650 Neighboring gene MPRA-validated peak6202 silencer Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_90808 Neighboring gene MPRA-validated peak6203 silencer Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:148037044-148037544 Neighboring gene uncharacterized LOC105378044 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:148225800-148226300 Neighboring gene uncharacterized LOC124901423 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr6:148467567-148468766 Neighboring gene NANOG hESC enhancer GRCh37_chr6:148495187-148495773 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:148573377-148573878 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:148573879-148574378 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr6:148585683-148586236 Neighboring gene SAM and SH3 domain containing 1 Neighboring gene RNA, U6 small nuclear 1222, pseudogene

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. Expression and localization of sterile alpha motif domain containing 5 is associated with cell type and malignancy of biliary tree. Yagai T, et al. PLoS One, 2017. PMID 28388653, Free PMC Article
  2. Common genetic variation and the control of HIV-1 in humans. Fellay J, et al. PLoS Genet, 2009 Dec. PMID 20041166, Free PMC Article
  3. BPA modulates the WDR5/TET2 complex to regulate ERβ expression in eutopic endometrium and drives the development of endometriosis. Xue W, et al. Environ Pollut, 2021 Jan 1. PMID 33022573
  4. 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
  5. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Strausberg RL, et al. Proc Natl Acad Sci U S A, 2002 Dec 24. PMID 12477932, Free PMC Article

See all (6) citations in PubMed

GeneRIFs: Gene References Into Functions

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

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

Gene Ontology Provided by GOA

Component Evidence Code Pubs
located_in cytoplasm IDA
Inferred from Direct Assay
more info
 PubMed 

General protein information

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Preferred Names
sterile alpha motif domain-containing protein 5
Names
SAM domain containing 1
SAM domain-containing protein 5

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_001030060.3 → NP_001025231.1  sterile alpha motif domain-containing protein 5

    See identical proteins and their annotated locations for NP_001025231.1

    Status: VALIDATED

    Source sequence(s)
    AL034350, AL354880, BX642659, CB988162
    Consensus CDS
    CCDS34548.1
    UniProtKB/Swiss-Prot
    Q5TGI4
    Related
    ENSP00000356444.1, ENST00000367474.2
    Conserved Domains (2) summary
    cd09527
    Location:2 → 64
    SAM_Samd5; SAM domain of Samd5 subfamily
    smart00454
    Location:6 → 65
    SAM; Sterile alpha motif

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_000006.12 Reference GRCh38.p14 Primary Assembly

    Range
    147508690..147954680
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017010850.2 → XP_016866339.1  sterile alpha motif domain-containing protein 5 isoform X1

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060930.1 Alternate T2T-CHM13v2.0

    Range
    148701984..149150652
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054355417.1 → XP_054211392.1  sterile alpha motif domain-containing protein 5 isoform X1

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q5TGI4.1 GenPept UniProtKB/Swiss-Prot:Q5TGI4

Gene LinkOut

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

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