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

    Gene ID: 27164, updated on 28-Oct-2024

    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; AllianceGenome:HGNC:10527
    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
    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
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See SALL3 in Genome Data Viewer
    Location:
    18q23
    Exon count:
    3
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 18 NC_000018.10 (78979818..78998969)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 18 NC_060942.1 (79214396..79233545)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 18 NC_000018.9 (76739818..76758969)

    Chromosome 18 - NC_000018.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105372224 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr18:76669815-76671014 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr18:76686389-76687588 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr18:76694205-76695173 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr18:76695174-76696141 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr18:76707071-76707585 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr18:76732217-76732814 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr18:76732815-76733411 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr18:76736667-76737380 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr18:76741235-76742064 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr18:76743410-76744168 Neighboring gene NANOG hESC enhancer GRCh37_chr18:76744863-76745377 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr18:76753804-76754785 Neighboring gene long intergenic non-protein coding RNA 1896 Neighboring gene uncharacterized LOC105372225 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr18:76766909-76768108 Neighboring gene ReSE screen-validated silencer GRCh37_chr18:76816919-76817092 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr18:76819471-76819970 Neighboring gene ATPase phospholipid transporting 9B (putative) Neighboring gene uncharacterized LOC124904331 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr18:76905122-76905630 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr18:76905631-76906137

    Genomic regions, transcripts, and products

    Expression

    • Project title: HPA RNA-seq normal tissues 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
    Genome-wide association for abdominal subcutaneous and visceral adipose reveals a novel locus for visceral fat in women.
    EBI GWAS Catalog
    Genome-wide association study of rheumatoid arthritis in the Spanish population: KLF12 as a risk locus for rheumatoid arthritis susceptibility.
    EBI GWAS Catalog
    Identification of 23 new prostate cancer susceptibility loci using the iCOGS custom genotyping array.
    EBI GWAS Catalog

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables DNA-binding transcription factor activity, RNA polymerase II-specific IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables RNA polymerase II cis-regulatory region sequence-specific DNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
     
    Process Evidence Code Pubs
    involved_in regulation of transcription by RNA polymerase II IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    Component Evidence Code Pubs
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
     

    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)

    NEW Try the new Transcript table

    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
      4544..23695
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_171999.4NP_741996.2  sal-like protein 3

      See identical proteins and their annotated locations for NP_741996.2

      Status: VALIDATED

      Source sequence(s)
      AC099689
      Consensus CDS
      CCDS12013.1
      UniProtKB/Swiss-Prot
      Q9BXA9, Q9UGH1
      UniProtKB/TrEMBL
      A0A140TA70, A0A384MEH2
      Related
      ENSP00000441823.2, ENST00000537592.7
      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: GCF_000001405.40-RS_2024_08

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000018.10 Reference GRCh38.p14 Primary Assembly

      Range
      78979818..78998969
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Reference GRCh38.p14 ALT_REF_LOCI_1

    Genomic

    1. NW_003315961.1 Reference GRCh38.p14 ALT_REF_LOCI_1

      Range
      44933..64085
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Reference GRCh38.p14 ALT_REF_LOCI_2

    Genomic

    1. NT_187666.1 Reference GRCh38.p14 ALT_REF_LOCI_2

      Range
      44933..64084
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060942.1 Alternate T2T-CHM13v2.0

      Range
      79214396..79233545
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)