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SALL3 spalt like transcription factor 3 [ Homo sapiens (human) ]

Gene ID: 27164, updated on 21-Aug-2020

Summary

Official Symbol
SALL3provided by HGNC
Official Full Name
spalt like transcription factor 3provided by HGNC
Primary source
HGNC:HGNC:10527
See related
Ensembl:ENSG00000256463 MIM:605079
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
ZNF796
Summary
This gene encodes a sal-like C2H2-type zinc-finger protein, and belongs to a family of evolutionarily conserved genes found in species as diverse as Drosophila, C. elegans, and vertebrates. Mutations in some of these genes are associated with congenital disorders in human, suggesting their importance in embryonic development. This protein binds to DNA methyltransferase 3 alpha (DNMT3A), and reduces DNMT3A-mediated CpG island methylation. It is suggested that silencing of this gene, resulting in acceleration of DNA methylation, may have a role in oncogenesis. [provided by RefSeq, Oct 2011]
Expression
Biased expression in brain (RPKM 1.5), prostate (RPKM 0.7) and 2 other tissues See more
Orthologs

Genomic context

See SALL3 in Genome Data Viewer
Location:
18q23
Exon count:
3
Annotation release Status Assembly Chr Location
109.20200815 current GRCh38.p13 (GCF_000001405.39) 18 NC_000018.10 (78980275..78998969)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 18 NC_000018.9 (76740275..76759770)

Chromosome 18 - NC_000018.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105372224 Neighboring gene long intergenic non-protein coding RNA 1896 Neighboring gene uncharacterized LOC105372225 Neighboring gene ATPase phospholipid transporting 9B (putative) Neighboring gene VISTA enhancer hs775

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

Associated conditions

Description Tests
Genome-wide association for abdominal subcutaneous and visceral adipose reveals a novel locus for visceral fat in women.
GeneReviews: Not available
Genome-wide association study of rheumatoid arthritis in the Spanish population: KLF12 as a risk locus for rheumatoid arthritis susceptibility.
GeneReviews: Not available
Identification of 23 new prostate cancer susceptibility loci using the iCOGS custom genotyping array.
GeneReviews: Not available

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
DNA binding IEA
Inferred from Electronic Annotation
more info
 
DNA-binding transcription factor activity, RNA polymerase II-specific IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
metal ion binding IEA
Inferred from Electronic Annotation
more info
 
transcription regulatory region sequence-specific DNA binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
Process Evidence Code Pubs
forelimb morphogenesis IEA
Inferred from Electronic Annotation
more info
 
hindlimb morphogenesis IEA
Inferred from Electronic Annotation
more info
 
negative regulation of smoothened signaling pathway IEA
Inferred from Electronic Annotation
more info
 
olfactory bulb interneuron development IEA
Inferred from Electronic Annotation
more info
 
regulation of transcription by RNA polymerase II IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
Component Evidence Code Pubs
nucleus IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 

General protein information

Preferred Names
sal-like protein 3
Names
C2H2 zinc finger protein SALL3
epididymis secretory sperm binding protein
hSALL3
spalt-like zinc finger protein
zinc finger protein 796

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.

Genomic

  1. NG_030353.1 RefSeqGene

    Range
    5001..23695
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_171999.3NP_741996.2  sal-like protein 3

    See identical proteins and their annotated locations for NP_741996.2

    Status: REVIEWED

    Source sequence(s)
    AC099689, AI569735, AW956238, BC148296
    Consensus CDS
    CCDS12013.1
    UniProtKB/Swiss-Prot
    Q9BXA9
    UniProtKB/TrEMBL
    A9JR48
    Related
    ENSP00000441823.2, ENST00000537592.6
    Conserved Domains (4) summary
    COG5048
    Location:412734
    COG5048; FOG: Zn-finger [General function prediction only]
    sd00017
    Location:681701
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam00096
    Location:11431163
    zf-C2H2; Zinc finger, C2H2 type
    pfam13465
    Location:693718
    zf-H2C2_2; Zinc-finger double domain

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.20200815

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000018.10 Reference GRCh38.p13 Primary Assembly

    Range
    78980275..78998969
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p13 ALT_REF_LOCI_1

Genomic

  1. NW_003315961.1 Reference GRCh38.p13 ALT_REF_LOCI_1

    Range
    45390..64085
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p13 ALT_REF_LOCI_2

Genomic

  1. NT_187666.1 Reference GRCh38.p13 ALT_REF_LOCI_2

    Range
    45390..64084
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
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