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

Gene ID: 57167, updated on 28-Nov-2021

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
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
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Genomic context

See SALL4 in Genome Data Viewer
Location:
20q13.2
Exon count:
8
Annotation release Status Assembly Chr Location
109.20211119 current GRCh38.p13 (GCF_000001405.39) 20 NC_000020.11 (51782331..51802521, complement)
105.20201022 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 ATPase phospholipid transporting 9A (putative) Neighboring gene Sharpr-MPRA regulatory region 9373 Neighboring gene ribosomal protein L29 pseudogene Neighboring gene long intergenic non-protein coding RNA 1429 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
Cross-Disorder Genome-Wide Analyses Suggest a Complex Genetic Relationship Between Tourette's Syndrome and OCD.
GeneReviews: Not available
Duane-radial ray syndrome
MedGen: C1623209 OMIM: 607323 GeneReviews: SALL4-Related Disorders
Compare labs
Genome-wide study of single-nucleotide polymorphisms associated with azoospermia and severe oligozoospermia.
GeneReviews: 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

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

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
PubMed 
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
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
PubMed 
involved_in 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
 
located_in 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
PubMed 
part_of protein-containing complex IEA
Inferred from Electronic Annotation
more info
 

General protein information

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

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.

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
    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: Homo sapiens Updated Annotation Release 109.20211119

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000020.11 Reference GRCh38.p13 Primary Assembly

    Range
    51782331..51802521 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
    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
    cd20908
    Location:279327
    SUF4-like; N-terminal domain of Oryza sativa transcription factor SUPPRESSOR OF FRI 4 (OsSUF4), Arabidopsis thaliana SUF4 (AtSUF4), and similar proteins
  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
    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
    cd20908
    Location:279327
    SUF4-like; N-terminal domain of Oryza sativa transcription factor SUPPRESSOR OF FRI 4 (OsSUF4), Arabidopsis thaliana SUF4 (AtSUF4), and similar proteins
  3. XM_005260467.4XP_005260524.1  sal-like protein 4 isoform X1

    See identical proteins and their annotated locations for XP_005260524.1

    Conserved Domains (4) summary
    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
    cd20908
    Location:279327
    SUF4-like; N-terminal domain of Oryza sativa transcription factor SUPPRESSOR OF FRI 4 (OsSUF4), Arabidopsis thaliana SUF4 (AtSUF4), and similar proteins
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