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

    Gene ID: 57167, updated on 22-Apr-2024

    Summary

    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; AllianceGenome:HGNC:15924
    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; IVIC; 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]
    Expression
    Biased expression in testis (RPKM 2.4), thyroid (RPKM 1.3) and 4 other tissues See more
    Orthologs
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See SALL4 in Genome Data Viewer
    Location:
    20q13.2
    Exon count:
    5
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 20 NC_000020.11 (51782331..51802521, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 20 NC_060944.1 (53553791..53573978, complement)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 20 NC_000020.10 (50398870..50419060, complement)

    Chromosome 20 - NC_000020.11Genomic Context describing neighboring genes Neighboring gene nuclear factor of activated T cells 2 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:50072771-50073376 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:50079139-50080099 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr20:50103914-50105113 Neighboring gene microRNA 3194 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:50105077-50105578 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18112 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18113 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18114 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr20:50149441-50150640 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:50157559-50158228 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13041 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13042 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:50186888-50187388 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr20:50224727-50225926 Neighboring gene ReSE screen-validated silencer GRCh37_chr20:50226387-50226540 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:50240809-50241341 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr20:50247413-50248612 Neighboring gene Sharpr-MPRA regulatory region 9373 Neighboring gene ATPase phospholipid transporting 9A (putative) Neighboring gene Sharpr-MPRA regulatory region 11561 Neighboring gene H3K27ac hESC enhancer GRCh37_chr20:50315099-50315599 Neighboring gene Sharpr-MPRA regulatory region 2244 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:50318515-50319015 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr20:50321824-50322382 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:50323455-50323954 Neighboring gene NANOG hESC enhancer GRCh37_chr20:50327032-50327577 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:50329473-50329983 Neighboring gene Sharpr-MPRA regulatory region 2265 Neighboring gene Sharpr-MPRA regulatory region 2507 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:50366388-50366998 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:50378781-50379465 Neighboring gene ribosomal protein L29 pseudogene 35 Neighboring gene H3K27ac hESC enhancer GRCh37_chr20:50405009-50405510 Neighboring gene H3K27ac hESC enhancer GRCh37_chr20:50405511-50406010 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:50406470-50407036 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:50407037-50407602 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:50411851-50412350 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:50415843-50416766 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18116 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:50417479-50418121 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr20:50418765-50419406 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr20:50427387-50428259 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:50463018-50463518 Neighboring gene long intergenic non-protein coding RNA 1429 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:50478941-50479507 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:50503748-50504248 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:50504249-50504749 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:50509256-50509756 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:50509757-50510257 Neighboring gene RNA, U6 small nuclear 347, pseudogene

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

    Copy number response

    Description
    Copy number response
    Triplosensitivity

    No evidence available (Last evaluated 2021-01-11)

    ClinGen Genome Curation Page
    Haploinsufficency

    Sufficient evidence for dosage pathogenicity (Last evaluated 2021-01-11)

    ClinGen Genome Curation PagePubMed

    EBI GWAS Catalog

    Description
    Cross-Disorder Genome-Wide Analyses Suggest a Complex Genetic Relationship Between Tourette's Syndrome and OCD.
    EBI GWAS Catalog
    Genome-wide study of single-nucleotide polymorphisms associated with azoospermia and severe oligozoospermia.
    EBI GWAS Catalog

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Clone Names

    • MGC133050, dJ1112F19.1

    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
     
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    Process Evidence Code Pubs
    involved_in embryonic limb morphogenesis IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in inner cell mass cell proliferation IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in negative regulation of transcription by RNA polymerase II IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in neural tube closure IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in positive regulation of transcription by RNA polymerase II IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in regulation of transcription by RNA polymerase II IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in somatic stem cell population maintenance IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in ventricular septum development IEA
    Inferred from Electronic Annotation
    more info
     
    Component Evidence Code Pubs
    located_in cytoplasm IEA
    Inferred from Electronic Annotation
    more info
     
    part_of heterochromatin IEA
    Inferred from Electronic Annotation
    more info
     
    located_in intracellular membrane-bounded organelle IDA
    Inferred from Direct Assay
    more info
     
    located_in nucleoplasm IDA
    Inferred from Direct Assay
    more info
     
    located_in nucleoplasm TAS
    Traceable Author Statement
    more info
     
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
     

    General protein information

    Preferred Names
    sal-like protein 4
    Names
    zinc finger protein 797
    zinc finger protein SALL4

    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_008000.1 RefSeqGene

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

    mRNA and Protein(s)

    1. NM_001318031.2NP_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, ENST00000395997.3
      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_020436.5NP_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
      A2A2D8, Q540H3, Q6Y8G6, Q9UJQ4
      Related
      ENSP00000217086.4, ENST00000217086.9
      Conserved Domains (3) summary
      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: GCF_000001405.40-RS_2023_10

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000020.11 Reference GRCh38.p14 Primary Assembly

      Range
      51782331..51802521 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047440318.1XP_047296274.1  sal-like protein 4 isoform X1

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060944.1 Alternate T2T-CHM13v2.0

      Range
      53553791..53573978 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054323742.1XP_054179717.1  sal-like protein 4 isoform X1