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    SALL4 spalt like transcription factor 4 [ Homo sapiens (human) ]

    Gene ID: 57167, updated on 4-Jun-2017
    Official Symbol
    SALL4provided by HGNC
    Official Full Name
    spalt like transcription factor 4provided by HGNC
    Primary source
    HGNC:HGNC:15924
    See related
    Ensembl:ENSG00000101115 MIM:607343; Vega:OTTHUMG00000032752
    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
    DRRS; HSAL4; ZNF797
    Summary
    This gene encodes a zinc finger transcription factor thought to play a role in the development of abducens motor neurons. Defects in this gene are a cause of Duane-radial ray syndrome (DRRS). Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Dec 2015]
    Orthologs
    Location:
    20q13.2
    Exon count:
    8
    Annotation release Status Assembly Chr Location
    108 current GRCh38.p7 (GCF_000001405.33) 20 NC_000020.11 (51782717..51802523, complement)
    105 previous assembly GRCh37.p13 (GCF_000001405.25) 20 NC_000020.10 (50400551..50419059, complement)

    Chromosome 20 - NC_000020.11Genomic Context describing neighboring genes Neighboring gene nuclear factor of activated T-cells 2 Neighboring gene microRNA 3194 Neighboring gene ATPase phospholipid transporting 9A (putative) Neighboring gene ribosomal protein L29 pseudogene Neighboring gene long intergenic non-protein coding RNA 1429 Neighboring gene RNA, U6 small nuclear 347, pseudogene

    • 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 Jun 15 11:32:44 2016

    GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

    Associated conditions

    Description Tests
    Duane-radial ray syndrome
    MedGen: C1623209 OMIM: 607323 GeneReviews: SALL4-Related Disorders
    Compare labs
    IVIC syndrome
    MedGen: C1327918 OMIM: 147750 GeneReviews: Not available
    Compare labs

    Copy number response

    Description
    Copy number response
    Triplosensitivity

    No evidence available (Last evaluated (2012-04-19)

    ClinGen Genome Curation Page
    Haploinsufficency

    Sufficient evidence for dosage pathogenicity (Last evaluated (2012-04-19)

    ClinGen Genome Curation PagePubMed

    NHGRI GWAS Catalog

    Description
    Cross-Disorder Genome-Wide Analyses Suggest a Complex Genetic Relationship Between Tourette's Syndrome and OCD.
    NHGRI GWA Catalog
    Genome-wide study of single-nucleotide polymorphisms associated with azoospermia and severe oligozoospermia.
    NHGRI GWA Catalog
    Products Interactant Other Gene Complex Source Pubs Description

    Markers

    Homology

    Clone Names

    • MGC133050, dJ1112F19.1

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    metal ion binding IEA
    Inferred from Electronic Annotation
    more info
     
    protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    sequence-specific DNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    transcription factor activity, sequence-specific DNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    transcription factor binding IEA
    Inferred from Electronic Annotation
    more info
     
    transcription regulatory region DNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    Process Evidence Code Pubs
    embryonic limb morphogenesis IEA
    Inferred from Electronic Annotation
    more info
     
    inner cell mass cell proliferation IEA
    Inferred from Electronic Annotation
    more info
     
    negative regulation of transcription from RNA polymerase II promoter IEA
    Inferred from Electronic Annotation
    more info
     
    neural tube closure IEA
    Inferred from Electronic Annotation
    more info
     
    neurogenesis IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    positive regulation of transcription from RNA polymerase II promoter IEA
    Inferred from Electronic Annotation
    more info
     
    regulation of transcription, DNA-templated IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    signal transduction IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    somatic stem cell population maintenance TAS
    Traceable Author Statement
    more info
     
    transcription from RNA polymerase II promoter IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    ventricular septum development IEA
    Inferred from Electronic Annotation
    more info
     
    Component Evidence Code Pubs
    cytoplasm IEA
    Inferred from Electronic Annotation
    more info
     
    heterochromatin IEA
    Inferred from Electronic Annotation
    more info
     
    intracellular membrane-bounded organelle IDA
    Inferred from Direct Assay
    more info
     
    nucleoplasm IDA
    Inferred from Direct Assay
    more info
     
    nucleoplasm TAS
    Traceable Author Statement
    more info
     
    nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    protein complex IEA
    Inferred from Electronic Annotation
    more info
     
    Preferred Names
    sal-like protein 4
    Names
    zinc finger protein 797
    zinc finger protein SALL4

    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_008000.1 RefSeqGene

      Range
      5001..23468
      Download
      GenBank, FASTA, Sequence Viewer (Graphics), LRG_675

    mRNA and Protein(s)

    1. NM_001318031.1NP_001304960.1  sal-like protein 4 isoform 2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) uses an alternate in-frame splice site in the 3' coding region compared to variant 1. The encoded isoform (2) is shorter than isoform 1.
      Source sequence(s)
      AA419623, AA854044, AI638036, AL034420, AY170621, AY172738, BE549760, CN271900, DA666635, DA747867
      Consensus CDS
      CCDS82629.1
      UniProtKB/Swiss-Prot
      Q9UJQ4
      Related
      ENSP00000379319.3, OTTHUMP00000165811, ENST00000395997.3, OTTHUMT00000258918
      Conserved Domains (3) summary
      sd00017
      Location:435455
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam00096
      Location:435455
      zf-C2H2; Zinc finger, C2H2 type
      pfam13465
      Location:447472
      zf-H2C2_2; Zinc-finger double domain
    2. NM_020436.4NP_065169.1  sal-like protein 4 isoform 1

      See identical proteins and their annotated locations for NP_065169.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
      Source sequence(s)
      AA419623, AA854044, AI638036, AL034420, AY172738, BE549760, CN271900, DA666635, DA747867
      Consensus CDS
      CCDS13438.1
      UniProtKB/Swiss-Prot
      Q9UJQ4
      Related
      ENSP00000217086.4, OTTHUMP00000031296, ENST00000217086.8, OTTHUMT00000079738
      Conserved Domains (4) summary
      cd11674
      Location:791891
      lambda-1; inner capsid protein lambda-1 or VP3
      sd00017
      Location:568588
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam00096
      Location:626648
      zf-C2H2; Zinc finger, C2H2 type
      pfam13465
      Location:580605
      zf-H2C2_2; Zinc-finger double domain

    RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 108 details...Open this link in a new tab

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

    Reference GRCh38.p7 Primary Assembly

    Genomic

    1. NC_000020.11 Reference GRCh38.p7 Primary Assembly

      Range
      51782717..51802523 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011528921.2XP_011527223.1  sal-like protein 4 isoform X1

      See identical proteins and their annotated locations for XP_011527223.1

      Conserved Domains (4) summary
      cd11674
      Location:689789
      lambda-1; inner capsid protein lambda-1 or VP3
      sd00017
      Location:466486
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam00096
      Location:524546
      zf-C2H2; Zinc finger, C2H2 type
      pfam13465
      Location:478503
      zf-H2C2_2; Zinc-finger double domain
    2. XM_011528922.2XP_011527224.1  sal-like protein 4 isoform X1

      See identical proteins and their annotated locations for XP_011527224.1

      Conserved Domains (4) summary
      cd11674
      Location:689789
      lambda-1; inner capsid protein lambda-1 or VP3
      sd00017
      Location:466486
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam00096
      Location:524546
      zf-C2H2; Zinc finger, C2H2 type
      pfam13465
      Location:478503
      zf-H2C2_2; Zinc-finger double domain
    3. XM_005260467.3XP_005260524.1  sal-like protein 4 isoform X1

      See identical proteins and their annotated locations for XP_005260524.1

      Conserved Domains (4) summary
      cd11674
      Location:689789
      lambda-1; inner capsid protein lambda-1 or VP3
      sd00017
      Location:466486
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam00096
      Location:524546
      zf-C2H2; Zinc finger, C2H2 type
      pfam13465
      Location:478503
      zf-H2C2_2; Zinc-finger double domain

    Alternate CHM1_1.1

    Genomic

    1. NC_018931.2 Alternate CHM1_1.1

      Range
      50304150..50323951 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
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