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SAMD4A sterile alpha motif domain containing 4A [ Homo sapiens (human) ]

Gene ID: 23034, updated on 12-Oct-2019

Summary

Official Symbol
SAMD4Aprovided by HGNC
Official Full Name
sterile alpha motif domain containing 4Aprovided by HGNC
Primary source
HGNC:HGNC:23023
See related
Ensembl:ENSG00000020577 MIM:610747
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
SMG; SMGA; SAMD4; SMAUG; SMAUG1
Summary
Sterile alpha motifs (SAMs) in proteins such as SAMD4A are part of an RNA-binding domain that functions as a posttranscriptional regulator by binding to an RNA sequence motif known as the Smaug recognition element, which was named after the Drosophila Smaug protein (Baez and Boccaccio, 2005 [PubMed 16221671]).[supplied by OMIM, Mar 2008]
Expression
Broad expression in testis (RPKM 19.6), heart (RPKM 19.4) and 22 other tissues See more
Orthologs

Genomic context

See SAMD4A in Genome Data Viewer
Location:
14q22.2
Exon count:
16
Annotation release Status Assembly Chr Location
109.20190905 current GRCh38.p13 (GCF_000001405.39) 14 NC_000014.9 (54567097..54793315)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 14 NC_000014.8 (55033815..55260033)

Chromosome 14 - NC_000014.9Genomic Context describing neighboring genes Neighboring gene glia maturation factor beta Neighboring gene cell growth regulator with ring finger domain 1 Neighboring gene uncharacterized LOC112268133 Neighboring gene uncharacterized LOC729451 Neighboring gene RNA, U6atac small nuclear 9, pseudogene Neighboring gene GTP cyclohydrolase 1 Neighboring gene microRNA 4308

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

Bibliography

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Phenotypes

NHGRI GWAS Catalog

Description
Gene network analysis in a pediatric cohort identifies novel lung function genes.
NHGRI GWA Catalog
Novel genetic loci identified for the pathophysiology of childhood obesity in the Hispanic population.
NHGRI GWA Catalog

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • KIAA1053, DKFZp434H0350, DKFZp686A1532

Gene Ontology Provided by GOA

Function Evidence Code Pubs
RNA binding HDA PubMed 
mRNA binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
translation repressor activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
translation repressor activity IDA
Inferred from Direct Assay
more info
PubMed 
Process Evidence Code Pubs
negative regulation of translation IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
nuclear-transcribed mRNA poly(A) tail shortening IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
positive regulation of translation IDA
Inferred from Direct Assay
more info
PubMed 
regulation of mRNA stability IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
Component Evidence Code Pubs
P-body IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
cell junction IDA
Inferred from Direct Assay
more info
 
cytosol IDA
Inferred from Direct Assay
more info
 
dendrite IEA
Inferred from Electronic Annotation
more info
 
fibrillar center IDA
Inferred from Direct Assay
more info
 
synapse IEA
Inferred from Electronic Annotation
more info
 

General protein information

Preferred Names
protein Smaug homolog 1
Names
SAM domain-containing protein 4A

NCBI Reference Sequences (RefSeq)

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_001161576.2NP_001155048.2  protein Smaug homolog 1 isoform 2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) lacks an alternate in-frame exon in the central coding region, compared to variant 1, resulting in an isoform (2) that is shorter than isoform 1.
    Source sequence(s)
    AB028976, AK074716, AW129053, BC121174, DA393986
    Consensus CDS
    CCDS55917.2
    UniProtKB/Swiss-Prot
    Q9UPU9
    Related
    ENSP00000251091.5, ENST00000251091.9
    Conserved Domains (2) summary
    cd09557
    Location:238294
    SAM_Smaug; SAM domain of Smaug subfamily
    smart00454
    Location:236295
    SAM; Sterile alpha motif
  2. NM_001161577.2NP_001155049.1  protein Smaug homolog 1 isoform 3

    See identical proteins and their annotated locations for NP_001155049.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) differs in the 5' UTR, lacks a portion of the 5' coding region, initiates translation at a downstream start codon, and includes an alternate in-frame exon in the 3' coding region, compared to variant 1. The encoded isoform (3) is shorter than isoform 1.
    Source sequence(s)
    AB028976, AL133444, AW129053, BC011489, BC021726
    Consensus CDS
    CCDS55918.1
    UniProtKB/Swiss-Prot
    Q9UPU9
    UniProtKB/TrEMBL
    G3V2R1, Q8WW19
    Related
    ENSP00000450808.1, ENST00000555192.1
  3. NM_015589.6NP_056404.4  protein Smaug homolog 1 isoform 1

    See identical proteins and their annotated locations for NP_056404.4

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
    Source sequence(s)
    AB028976, AK024652, AK074716, AL133444, AL359792, BC121174, DA393986
    Consensus CDS
    CCDS32084.2
    UniProtKB/Swiss-Prot
    Q9UPU9
    Related
    ENSP00000452535.1, ENST00000554335.5
    Conserved Domains (2) summary
    cd09557
    Location:320382
    SAM_Smaug; SAM domain of Smaug subfamily
    smart00454
    Location:325383
    SAM; Sterile alpha motif

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109.20190905

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000014.9 Reference GRCh38.p13 Primary Assembly

    Range
    54567097..54793315
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_024449515.1XP_024305283.1  protein Smaug homolog 1 isoform X1

    Conserved Domains (1) summary
    cd09557
    Location:320382
    SAM_Smaug; SAM domain of Smaug subfamily
  2. XM_024449514.1XP_024305282.1  protein Smaug homolog 1 isoform X1

    Conserved Domains (1) summary
    cd09557
    Location:320382
    SAM_Smaug; SAM domain of Smaug subfamily
  3. XM_024449516.1XP_024305284.1  protein Smaug homolog 1 isoform X2

    Conserved Domains (1) summary
    cd09557
    Location:320382
    SAM_Smaug; SAM domain of Smaug subfamily
  4. XM_024449517.1XP_024305285.1  protein Smaug homolog 1 isoform X3

    Conserved Domains (1) summary
    cd09557
    Location:238294
    SAM_Smaug; SAM domain of Smaug subfamily
  5. XM_024449518.1XP_024305286.1  protein Smaug homolog 1 isoform X4

    Conserved Domains (1) summary
    cd09557
    Location:219281
    SAM_Smaug; SAM domain of Smaug subfamily
  6. XM_024449519.1XP_024305287.1  protein Smaug homolog 1 isoform X5

    Conserved Domains (1) summary
    cd09557
    Location:137193
    SAM_Smaug; SAM domain of Smaug subfamily
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