Sall4 (spalt-like transcription factor 4) - Rat Genome Database

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Gene: Sall4 (spalt-like transcription factor 4) Rattus norvegicus
Symbol: Sall4
Name: spalt-like transcription factor 4
RGD ID: 1597672
Description: Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Predicted to be involved in regulation of transcription by RNA polymerase II. Predicted to act upstream of or within several processes, including chordate embryonic development; embryonic limb morphogenesis; and regulation of transcription by RNA polymerase II. Predicted to be located in nucleoplasm. Predicted to be part of heterochromatin. Predicted to be active in nucleus. Human ortholog(s) of this gene implicated in Duane retraction syndrome; Duane-radial ray syndrome; Holt-Oram syndrome; IVIC syndrome; and ventricular septal defect. Orthologous to human SALL4 (spalt like transcription factor 4); INTERACTS WITH aflatoxin B1; azoxystrobin; bisphenol A.
Type: protein-coding
RefSeq Status: MODEL
Previously known as: LOC686412; sal-like 4; sal-like 4 (Drosophila); sal-like protein 4; similar to sal-like 4 isoform a
RGD Orthologs
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Rat AssemblyChrPosition (strand)SourceGenome Browsers
mRatBN7.23157,474,067 - 157,491,055 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl3157,474,642 - 157,490,822 (-)EnsemblmRatBN7.2 Ensembl
Rnor_6.03165,520,155 - 165,538,176 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl3165,520,392 - 165,537,940 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.03171,656,504 - 171,674,423 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Celera3156,038,840 - 156,055,436 (-)NCBICelera
Cytogenetic Map3q42NCBI
JBrowse: View Region in Genome Browser (JBrowse)


References - curated
# Reference Title Reference Citation
1. Duane radial ray syndrome (Okihiro syndrome) maps to 20q13 and results from mutations in SALL4, a new member of the SAL family. Al-Baradie R, etal., Am J Hum Genet. 2002 Nov;71(5):1195-9. Epub 2002 Oct 22.
2. Novel frameshift variant in gene SALL4 causing Okihiro syndrome. Alves LU, etal., Eur J Med Genet. 2016 Feb;59(2):80-5. doi: 10.1016/j.ejmg.2015.12.015. Epub 2016 Jan 11.
3. Sall1, sall2, and sall4 are required for neural tube closure in mice. Bohm J, etal., Am J Pathol. 2008 Nov;173(5):1455-63. doi: 10.2353/ajpath.2008.071039. Epub 2008 Sep 25.
4. SALL4 is a novel diagnostic marker for testicular germ cell tumors. Cao D, etal., Am J Surg Pathol. 2009 Jul;33(7):1065-77. doi: 10.1097/PAS.0b013e3181a13eef.
5. SALL4 is a novel sensitive and specific marker of ovarian primitive germ cell tumors and is particularly useful in distinguishing yolk sac tumor from clear cell carcinoma. Cao D, etal., Am J Surg Pathol. 2009 Jun;33(6):894-904. doi: 10.1097/PAS.0b013e318198177d.
6. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
7. SALL4 is a marker of the embryonal subtype of hepatoblastoma. Gnemmi V, etal., Histopathology. 2013 Sep;63(3):425-8. doi: 10.1111/his.12187. Epub 2013 Jul 3.
8. Immunohistochemical expression of SALL4 in hepatocellular carcinoma, a potential pitfall in the differential diagnosis of yolk sac tumors. Gonzalez-Roibon N, etal., Hum Pathol. 2013 Jul;44(7):1293-9. doi: 10.1016/j.humpath.2012.10.017. Epub 2013 Jan 21.
9. Okihiro syndrome is caused by SALL4 mutations. Kohlhase J, etal., Hum Mol Genet. 2002 Nov 1;11(23):2979-87.
10. Mutations at the SALL4 locus on chromosome 20 result in a range of clinically overlapping phenotypes, including Okihiro syndrome, Holt-Oram syndrome, acro-renal-ocular syndrome, and patients previously reported to represent thalidomide embryopathy. Kohlhase J, etal., J Med Genet. 2003 Jul;40(7):473-8.
11. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
12. GOA pipeline RGD automated data pipeline
13. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
14. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
15. Comprehensive gene review and curation RGD comprehensive gene curation
16. The murine homolog of SALL4, a causative gene in Okihiro syndrome, is essential for embryonic stem cell proliferation, and cooperates with Sall1 in anorectal, heart, brain and kidney development. Sakaki-Yumoto M, etal., Development. 2006 Aug;133(15):3005-13. doi: 10.1242/dev.02457. Epub 2006 Jun 21.
17. A family with features overlapping Okihiro syndrome, hemifacial microsomia and isolated Duane anomaly caused by a novel SALL4 mutation. Terhal P, etal., Am J Med Genet A. 2006 Feb 1;140(3):222-6.
18. Genetic variation of SAL-Like 4 (SALL4) in ventricular septal defect. Wang B, etal., Int J Cardiol. 2010 Nov 19;145(2):224-6. doi: 10.1016/j.ijcard.2009.05.067. Epub 2009 Jul 19.
19. A Sall4 mutant mouse model useful for studying the role of Sall4 in early embryonic development and organogenesis. Warren M, etal., Genesis. 2007 Jan;45(1):51-8.
20. Diversified clinical presentations associated with a novel sal-like 4 gene mutation in a Chinese pedigree with Duane retraction syndrome. Yang MM, etal., Mol Vis. 2013 May 6;19:986-94. Print 2013.
Additional References at PubMed
PMID:16380715   PMID:17060609   PMID:17295837   PMID:19796622   PMID:20720539   PMID:26523946  


Comparative Map Data
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
mRatBN7.23157,474,067 - 157,491,055 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl3157,474,642 - 157,490,822 (-)EnsemblmRatBN7.2 Ensembl
Rnor_6.03165,520,155 - 165,538,176 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl3165,520,392 - 165,537,940 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.03171,656,504 - 171,674,423 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Celera3156,038,840 - 156,055,436 (-)NCBICelera
Cytogenetic Map3q42NCBI
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
GRCh382051,782,331 - 51,802,521 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl2051,782,331 - 51,802,521 (-)EnsemblGRCh38hg38GRCh38
GRCh372050,398,870 - 50,419,060 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 362049,833,988 - 49,852,421 (-)NCBINCBI36Build 36hg18NCBI36
Build 342049,833,991 - 49,852,421NCBI
Celera2047,105,283 - 47,123,757 (-)NCBICelera
Cytogenetic Map20q13.2NCBI
HuRef2047,147,931 - 47,166,405 (-)NCBIHuRef
CHM1_12050,305,475 - 50,323,937 (-)NCBICHM1_1
T2T-CHM13v2.02053,553,791 - 53,573,978 (-)NCBIT2T-CHM13v2.0
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
GRCm392168,590,252 - 168,609,121 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl2168,590,252 - 168,609,863 (-)EnsemblGRCm39 Ensembl
GRCm382168,748,332 - 168,767,201 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl2168,748,332 - 168,767,943 (-)EnsemblGRCm38mm10GRCm38
MGSCv372168,573,832 - 168,592,701 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv362168,440,991 - 168,458,333 (-)NCBIMGSCv36mm8
Celera2174,694,286 - 174,713,507 (-)NCBICelera
Cytogenetic Map2H3NCBI
cM Map288.99NCBI
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
ChiLan1.0 EnsemblNW_0049554456,824,770 - 6,842,187 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554456,824,797 - 6,841,141 (+)NCBIChiLan1.0ChiLan1.0
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
NHGRI_mPanPan12057,529,106 - 57,549,399 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v02048,130,387 - 48,150,569 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.12049,252,320 - 49,272,973 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl2049,254,039 - 49,273,589 (-)Ensemblpanpan1.1panPan2
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
CanFam3.12437,941,498 - 37,959,713 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2437,940,034 - 38,037,287 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2437,180,959 - 37,200,584 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.02438,651,355 - 38,669,523 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl2438,649,920 - 38,749,658 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.12437,887,041 - 37,905,946 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.02438,020,086 - 38,039,234 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.02438,565,716 - 38,585,336 (-)NCBIUU_Cfam_GSD_1.0
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
HiC_Itri_2NW_024408640187,831,936 - 187,849,998 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049365143,285,531 - 3,303,644 (+)EnsemblSpeTri2.0
SpeTri2.0NW_0049365143,285,778 - 3,302,179 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
Sscrofa11.1 Ensembl1753,084,310 - 53,103,190 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11753,082,610 - 53,103,023 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21759,526,086 - 59,533,416 (-)NCBISscrofa10.2Sscrofa10.2susScr3
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
ChlSab1.1212,179,721 - 12,199,629 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl212,182,357 - 12,199,321 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366605060,576,222 - 60,593,578 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
HetGla_female_1.0 EnsemblNW_0046247904,162,454 - 4,170,923 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046247904,153,157 - 4,170,813 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2


Variants in Sall4
55 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:64
Count of miRNA genes:30
Interacting mature miRNAs:32
Transcripts:ENSRNOT00000070964, ENSRNOT00000071119
Prediction methods:Miranda, Rnahybrid, Targetscan
Result types:miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (
For more information about miRGate, see PMID:25858286 or access the full paper here.

QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
70216Cm14Cardiac mass QTL 142.1heart mass (VT:0007028)heart wet weight (CMO:0000069)331172320163586636Rat
1559282Emca5Estrogen-induced mammary cancer QTL 53.9mammary gland integrity trait (VT:0010552)percentage of study population developing mammary tumors during a period of time (CMO:0000948)343827364169034231Rat
1581568Rf53Renal function QTL 53urine total protein amount (VT:0000032)urine protein excretion rate to body weight ratio (CMO:0001099)356395968161299569Rat
631841Niddm39Non-insulin dependent diabetes mellitus QTL 393.36blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)394856903159898684Rat
2312659Slep7Serum leptin concentration QTL 70.001blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)398535255168026850Rat
2312670Bw94Body weight QTL 940.01inguinal fat pad mass (VT:0010424)inguinal fat pad weight to body weight ratio (CMO:0001253)398535255168026850Rat
2312673Scl63Serum cholesterol level QTL 630.001blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)398535255168026850Rat
2302373Gluco39Glucose level QTL 395.01blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)398535386161695835Rat
1578754Stresp16Stress response QTL 1640.001blood renin amount (VT:0003349)plasma renin activity level (CMO:0000116)3112681431157681431Rat
1576306Schws3Schwannoma susceptibility QTL 30.001nervous system integrity trait (VT:0010566)percentage of study population developing trigeminal nerve neurilemmomas during a period of time (CMO:0002017)3118839124163839124Rat
1598877Bp285Blood pressure QTL 2851.50.03arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)3120538241165538241Rat
10755461Coatc16Coat color QTL 16coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)3122438700167438700Rat
631541Bp81Blood pressure QTL 814arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)3124122556169034231Rat
2303620Vencon4Ventilatory control QTL 43.9respiration trait (VT:0001943)tidal volume (CMO:0000222)3127162703168026850Rat
631673Iddm13Insulin dependent diabetes mellitus QTL 131.30.663blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)3130193298161695983Rat
1578656Vnigr2Vascular neointimal growth QTL 24.2artery morphology trait (VT:0002191)lesioned artery residual lumen area (CMO:0001417)3130656562169034231Rat
1578653Vnigr3Vascular neointimal growth QTL 33.1artery morphology trait (VT:0002191)artery neointimal hyperplastic lesion area (CMO:0001414)3130656562169034231Rat
9589106Insul23Insulin level QTL 2313.860.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)3131635904169034231Rat
2298477Eau4Experimental allergic uveoretinitis QTL 40.0011uvea integrity trait (VT:0010551)experimental autoimmune uveitis score (CMO:0001504)3137398739169034231Rat
8552952Pigfal13Plasma insulin-like growth factor 1 level QTL 13blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)3138799500169034231Rat
1298068Bp167Blood pressure QTL 1670.004arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)3141074471169034231Rat
1331726Bp208Blood pressure QTL 2083.129arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)3141339013162184794Rat
2317883Alcrsp26Alcohol response QTL 261.80.63response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)3145526770169034231Rat
12879871Am7Aortic mass QTL 70.001aorta mass (VT:0002845)aorta weight to aorta length to body weight ratio (CMO:0002722)3145925360166177555Rat
12879872Cm97Cardiac mass QTL 970.001heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)3145925360166177555Rat
12879873Cm96Cardiac mass QTL 960.001heart mass (VT:0007028)heart wet weight to body weight ratio (CMO:0002408)3145925360166177555Rat
12879874Cm98Cardiac mass QTL 980.005heart right ventricle mass (VT:0007033)heart right ventricle weight to body weight ratio (CMO:0000914)3145925360166177555Rat
12879875Kidm64Kidney mass QTL 640.001kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)3145925360166177555Rat
12879876Bw182Body weight QTL 1820.003body mass (VT:0001259)body weight (CMO:0000012)3145925360166177555Rat
2301411Bp320Blood pressure QTL 3200.001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)3145925360166177555Rat
1598854Memor10Memory QTL 102exploratory behavior trait (VT:0010471)average horizontal distance between subject and target during voluntary locomotion in an experimental apparatus (CMO:0002674)3145956084161299569Rat
8552791Vie2Viral induced encephalitis QTL 24.1brain integrity trait (VT:0010579)encephalitis incidence/prevalence measurement (CMO:0002361)3145956084169034231Rat
1578666Vnigr1Vascular neointimal growth QTL 14.6artery morphology trait (VT:0002191)artery lumen area (CMO:0001409)3149040888168026850Rat

Markers in Region
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.23157,474,128 - 157,474,212 (+)MAPPERmRatBN7.2
Rnor_6.03165,519,879 - 165,519,962NCBIRnor6.0
Rnor_5.03171,656,228 - 171,656,311UniSTSRnor5.0
Celera3156,038,564 - 156,038,647UniSTS


RNA-SEQ Expression
High: > 1000 TPM value   Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM   Below Cutoff: < 0.5 TPM

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
Medium 2 4 4 4 10 10
Low 33 21 21 21 1 4 25 14 19 1
Below cutoff 2 8 15 13 2 13 7 7 24 6 8 1 7


RefSeq Acc Id: ENSRNOT00000070964   ⟹   ENSRNOP00000066945
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl3157,474,642 - 157,490,822 (-)Ensembl
Rnor_6.0 Ensembl3165,520,392 - 165,537,940 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000071119   ⟹   ENSRNOP00000067726
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl3157,474,642 - 157,490,822 (-)Ensembl
Rnor_6.0 Ensembl3165,520,392 - 165,537,940 (-)Ensembl
RefSeq Acc Id: XM_003749632   ⟹   XP_003749680
Rat AssemblyChrPosition (strand)Source
mRatBN7.23157,474,067 - 157,491,055 (-)NCBI
Rnor_6.03165,520,155 - 165,538,176 (-)NCBI
Rnor_5.03171,656,504 - 171,674,423 (-)NCBI
Protein Sequences
Protein RefSeqs XP_003749680 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDL96356 (Get FASTA)   NCBI Sequence Viewer  
RefSeq Acc Id: XP_003749680   ⟸   XM_003749632
- UniProtKB: M0RDM1 (UniProtKB/TrEMBL),   A6JXQ3 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000066945   ⟸   ENSRNOT00000070964
RefSeq Acc Id: ENSRNOP00000067726   ⟸   ENSRNOT00000071119
Protein Domains

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-M0RDM1-F1-model_v2 AlphaFold M0RDM1 1-1070 view protein structure


eQTL   View at Phenogen
WGCNA   View at Phenogen
Tissue/Strain Expression   View at Phenogen

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1597672 AgrOrtholog
BioCyc Gene G2FUF-46693 BioCyc
Ensembl Genes ENSRNOG00000050035 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000066945.1 UniProtKB/TrEMBL
  ENSRNOP00000067726.1 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000070964.2 UniProtKB/TrEMBL
  ENSRNOT00000071119.4 UniProtKB/TrEMBL
Gene3D-CATH Classic Zinc Finger UniProtKB/TrEMBL
InterPro Znf_C2H2/integrase_DNA-bd UniProtKB/TrEMBL
  Znf_C2H2_sf UniProtKB/TrEMBL
KEGG Report rno:686412 UniProtKB/TrEMBL
Pfam zf-C2H2 UniProtKB/TrEMBL
PhenoGen Sall4 PhenoGen
Superfamily-SCOP SSF57667 UniProtKB/TrEMBL

Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2013-11-11 Sall4  spalt-like transcription factor 4  Sall4  sal-like 4 (Drosophila)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2013-08-16 Sall4  sal-like 4 (Drosophila)  LOC686412  similar to sal-like 4 isoform a  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-11-20 LOC686412  similar to sal-like 4 isoform a      Symbol and Name status set to provisional 70820 PROVISIONAL