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

Gene ID: 23034, updated on 13-Oct-2022

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; AllianceGenome:HGNC:23023
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
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Genomic context

See SAMD4A in Genome Data Viewer
Location:
14q22.2
Exon count:
18
Annotation release Status Assembly Chr Location
110 current GRCh38.p14 (GCF_000001405.40) 14 NC_000014.9 (54565316..54793315)
110 current T2T-CHM13v2.0 (GCF_009914755.1) 14 NC_060938.1 (48772324..48998510)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 14 NC_000014.8 (55033846..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 SAMD4A antisense RNA 1 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

EBI GWAS Catalog

Description
Gene network analysis in a pediatric cohort identifies novel lung function genes.
EBI GWAS Catalog
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

Clone Names

  • KIAA1053, DKFZp434H0350, DKFZp686A1532

Gene Ontology Provided by GOA

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

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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_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
    Q6PEW4, Q9UPU9
    Related
    ENSP00000452535.1, ENST00000554335.6
    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 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_000014.9 Reference GRCh38.p14 Primary Assembly

    Range
    54565316..54793315
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047431137.1XP_047287093.1  protein Smaug homolog 1 isoform X1

  2. XM_047431136.1XP_047287092.1  protein Smaug homolog 1 isoform X1

  3. XM_024449516.2XP_024305284.1  protein Smaug homolog 1 isoform X2

    Conserved Domains (1) summary
    cd09557
    Location:320382
    SAM_Smaug; SAM domain of Smaug subfamily
  4. XM_047431138.1XP_047287094.1  protein Smaug homolog 1 isoform X3

    UniProtKB/Swiss-Prot
    Q6PEW4
  5. XM_047431140.1XP_047287096.1  protein Smaug homolog 1 isoform X4

  6. XM_047431143.1XP_047287099.1  protein Smaug homolog 1 isoform X6

  7. XM_047431144.1XP_047287100.1  protein Smaug homolog 1 isoform X7

  8. XM_024449515.2XP_024305283.1  protein Smaug homolog 1 isoform X1

    Conserved Domains (1) summary
    cd09557
    Location:320382
    SAM_Smaug; SAM domain of Smaug subfamily
  9. XM_047431146.1XP_047287102.1  protein Smaug homolog 1 isoform X7

  10. XM_024449514.2XP_024305282.1  protein Smaug homolog 1 isoform X1

    Conserved Domains (1) summary
    cd09557
    Location:320382
    SAM_Smaug; SAM domain of Smaug subfamily
  11. XM_047431139.1XP_047287095.1  protein Smaug homolog 1 isoform X3

    UniProtKB/Swiss-Prot
    Q6PEW4
    Related
    ENSP00000375919.3, ENST00000392067.7
  12. XM_047431141.1XP_047287097.1  protein Smaug homolog 1 isoform X4

  13. XM_047431145.1XP_047287101.1  protein Smaug homolog 1 isoform X7

  14. XM_047431142.1XP_047287098.1  protein Smaug homolog 1 isoform X5

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060938.1 Alternate T2T-CHM13v2.0

    Range
    48772324..48998510
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)