Human Gene SALL4 (ENST00000371539.7) Description and Page Index
  Description: spalt like transcription factor 4 (from HGNC SALL4)
RefSeq Summary (NM_001318031): 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].
Gencode Transcript: ENST00000371539.7
Gencode Gene: ENSG00000101115.13
Transcript (Including UTRs)
   Position: hg38 chr20:51,784,046-51,802,509 Size: 18,464 Total Exon Count: 3 Strand: -
Coding Region
   Position: hg38 chr20:51,784,265-51,802,408 Size: 18,144 Coding Exon Count: 3 

Page IndexSequence and LinksMalaCardsCTDRNA-Seq ExpressionRNA Structure
Protein StructureOther SpeciesGO AnnotationsmRNA DescriptionsOther NamesGeneReviews
Methods
Data last updated: 2019-09-04

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr20:51,784,046-51,802,509)mRNA (may differ from genome)Protein (276 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaBioGPS
CGAPEnsemblExonPrimerGeneCardsHGNCLynx
MGIPubMedStanford SOURCEUniProtKBWikipedia

-  MalaCards Disease Associations
  MalaCards Gene Search: SALL4
Diseases sorted by gene-association score: duane-radial ray syndrome* (1723), ivic syndrome* (1278), okihiro syndrome due to a point mutation* (350), acro-renal-ocular syndrome* (119), sall4-related disorders* (100), okihiro syndrome due to 20q13 microdeletion* (25), duane retraction syndrome (18), spermatocytoma (16), combined thymoma (16), epithelioid trophoblastic tumor (15), hemifacial microsomia (11), placental site trophoblastic tumor (11), imperforate anus (10), holt-oram syndrome (10), radioulnar synostosis (8), epithelioid sarcoma (8), potter's syndrome (7), wolf-hirschhorn syndrome (7), blastoma (7), ovarian endodermal sinus tumor (7), ovarian primitive germ cell tumor (7), townes-brocks syndrome (6), extragonadal seminoma (6), endodermal sinus tumor (5), malignant teratoma (5), testicular yolk sac tumor (5), ovarian brenner tumor (4), ocular motility disease (4)
* = Manually curated disease association

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 3.93 RPKM in Thyroid
Total median expression: 13.81 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -35.30101-0.350 Picture PostScript Text
3' UTR -46.20219-0.211 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR007087 - Znf_C2H2
IPR015880 - Znf_C2H2-like
IPR013087 - Znf_C2H2/integrase_DNA-bd

ModBase Predicted Comparative 3D Structure on Q6Y8G5
FrontTopSide
The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
Genome BrowserGenome BrowserNo orthologNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
MGIRGD    
Protein SequenceProtein Sequence    
AlignmentAlignment    

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0003676 nucleic acid binding

Cellular Component:
GO:0005654 nucleoplasm


-  Descriptions from all associated GenBank mRNAs
  KJ899321 - Synthetic construct Homo sapiens clone ccsbBroadEn_08715 SALL4 gene, encodes complete protein.
KR711563 - Synthetic construct Homo sapiens clone CCSBHm_00025985 SALL4 (SALL4) mRNA, encodes complete protein.
KR711564 - Synthetic construct Homo sapiens clone CCSBHm_00025989 SALL4 (SALL4) mRNA, encodes complete protein.
AK001666 - Homo sapiens cDNA FLJ10804 fis, clone NT2RP4000837, weakly similar to Homo sapiens mRNA for zinc finger protein SALL1.
BC111714 - Homo sapiens sal-like 4 (Drosophila), mRNA (cDNA clone MGC:133050 IMAGE:40008661), complete cds.
AY170621 - Homo sapiens SALL4B mRNA, complete cds.
AY170622 - Homo sapiens SALL4C mRNA, complete cds.
AY172738 - Homo sapiens SALL4A protein mRNA, complete cds.
JD023063 - Sequence 4087 from Patent EP1572962.
JD032427 - Sequence 13451 from Patent EP1572962.
LF206038 - JP 2014500723-A/13541: Polycomb-Associated Non-Coding RNAs.
MA441615 - JP 2018138019-A/13541: Polycomb-Associated Non-Coding RNAs.

-  Other Names for This Gene
  Alternate Gene Symbols: AK001666, Q6Y8G5, Q6Y8G5_HUMAN, uc002xwi.1, uc002xwi.2, uc002xwi.3, uc002xwi.4, uc002xwi.5
UCSC ID: uc002xwi.5
RefSeq Accession: NM_001318031
Protein: Q6Y8G5

-  GeneReviews for This Gene
  GeneReviews article(s) related to gene SALL4:
drrs (SALL4-Related Disorders)
duane (Duane Syndrome)

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.