Sox21 (SRY-box transcription factor 21) - Rat Genome Database

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Gene: Sox21 (SRY-box transcription factor 21) Rattus norvegicus
Analyze
Symbol: Sox21
Name: SRY-box transcription factor 21
RGD ID: 1304724
Description: Predicted to enable DNA-binding transcription activator activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Predicted to be involved in positive regulation of transcription by RNA polymerase II and stem cell differentiation. Predicted to act upstream of or within hair follicle development and regulation of DNA-templated transcription. Predicted to be located in nucleus. Orthologous to human SOX21 (SRY-box transcription factor 21); INTERACTS WITH 6-propyl-2-thiouracil; bisphenol A; decabromodiphenyl ether.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: LOC306168; SRY (sex determining region Y)-box 21; SRY box 21; SRY-box containing gene 21; transcription factor SOX-21
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Pig
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr815101,699,580 - 101,703,175 (-)NCBIGRCr8
mRatBN7.21595,292,429 - 95,296,024 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1595,292,265 - 95,296,091 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1599,197,252 - 99,200,849 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.015100,329,208 - 100,332,805 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01597,257,882 - 97,261,479 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.015103,438,674 - 103,441,405 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl15103,440,212 - 103,441,030 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.015106,879,031 - 106,881,100 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.115103,137,749 - 103,215,460 (-)NCBI
Celera1594,143,028 - 94,146,136 (-)NCBICelera
Cytogenetic Map15q24NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component
nucleus  (IEA)

References

References - curated
# Reference Title Reference Citation
1. Rat ISS GO annotations from GOA human gene data--August 2006 GOA data from the GO Consortium
2. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
3. GOA pipeline RGD automated data pipeline
4. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:12446692   PMID:19470461   PMID:20876214  


Genomics

Comparative Map Data
Sox21
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr815101,699,580 - 101,703,175 (-)NCBIGRCr8
mRatBN7.21595,292,429 - 95,296,024 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1595,292,265 - 95,296,091 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1599,197,252 - 99,200,849 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.015100,329,208 - 100,332,805 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01597,257,882 - 97,261,479 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.015103,438,674 - 103,441,405 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl15103,440,212 - 103,441,030 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.015106,879,031 - 106,881,100 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.115103,137,749 - 103,215,460 (-)NCBI
Celera1594,143,028 - 94,146,136 (-)NCBICelera
Cytogenetic Map15q24NCBI
SOX21
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381394,709,622 - 94,712,545 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1394,709,622 - 94,712,545 (-)EnsemblGRCh38hg38GRCh38
GRCh371395,361,876 - 95,364,799 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361394,159,877 - 94,162,390 (-)NCBINCBI36Build 36hg18NCBI36
Build 341394,159,881 - 94,162,390NCBI
Celera1376,209,825 - 76,212,338 (-)NCBICelera
Cytogenetic Map13q32.1NCBI
HuRef1375,959,157 - 75,961,671 (-)NCBIHuRef
CHM1_11395,331,276 - 95,333,789 (-)NCBICHM1_1
T2T-CHM13v2.01393,913,127 - 93,916,050 (-)NCBIT2T-CHM13v2.0
Sox21
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm3914118,470,645 - 118,474,442 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl14118,470,644 - 118,474,442 (-)EnsemblGRCm39 Ensembl
GRCm3814118,233,233 - 118,237,030 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl14118,233,232 - 118,237,030 (-)EnsemblGRCm38mm10GRCm38
MGSCv3714118,632,455 - 118,636,252 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv3614117,116,943 - 117,119,608 (-)NCBIMGSCv36mm8
Celera14116,788,885 - 116,795,226 (-)NCBICelera
Cytogenetic Map14E4NCBI
cM Map1461.92NCBI
Sox21
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495540415,181,880 - 15,182,753 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495540415,181,866 - 15,184,317 (+)NCBIChiLan1.0ChiLan1.0
SOX21
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v21496,238,793 - 96,241,220 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11394,907,515 - 94,909,952 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01375,872,786 - 75,886,125 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
SOX21
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Dog10K_Boxer_Tasha2245,293,201 - 45,295,757 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.02245,937,673 - 45,940,223 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl2245,939,312 - 45,940,142 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.12245,590,821 - 45,593,354 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.02245,632,292 - 45,634,845 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.02245,641,650 - 45,644,164 (-)NCBIUU_Cfam_GSD_1.0
SOX21
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1163,825,637 - 63,826,467 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11163,822,110 - 63,826,498 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21169,963,743 - 69,968,603 (-)NCBISscrofa10.2Sscrofa10.2susScr3
SOX21
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1373,536,573 - 73,539,077 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl373,538,172 - 73,538,999 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366604629,926,237 - 29,929,157 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Sox21
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046248791,482,081 - 1,482,911 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046248791,480,436 - 1,483,000 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Sox21
15 total Variants

QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1578646Bmd18Bone mineral density QTL 185.2femur mineral mass (VT:0010011)trabecular volumetric bone mineral density (CMO:0001729)152280624098288169Rat
1578647Bmd17Bone mineral density QTL 174femur mineral mass (VT:0010011)total volumetric bone mineral density (CMO:0001728)152280624098288169Rat
1578660Bss19Bone structure and strength QTL 194.3femur morphology trait (VT:0000559)bone trabecular cross-sectional area (CMO:0002311)152280624098288169Rat
1300144Rf23Renal function QTL 233.61renal blood flow trait (VT:2000006)absolute change in renal vascular resistance (CMO:0001900)154063126898288169Rat
1576315Schws6Schwannoma susceptibility QTL 60.0069nervous system integrity trait (VT:0010566)post-insult time of death (CMO:0002005)155380615298806152Rat
631655Bp126Blood pressure QTL 1264arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1558156477101769107Rat
731177Uae26Urinary albumin excretion QTL 262.40.025urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)1567588667101769107Rat
2300326Plaw1Placental weight QTL 1150.005placenta mass (VT:0004257)placenta wet weight (CMO:0002088)1568327165100062518Rat
1641889Colcr6Colorectal carcinoma resistance QTL 62.90.0126intestine integrity trait (VT:0010554)benign colorectal tumor surface area measurement (CMO:0001799)157369051899794247Rat
2317055Aia10Adjuvant induced arthritis QTL 103.41joint integrity trait (VT:0010548)left rear ankle joint diameter (CMO:0002149)1575788062101769107Rat
1549844Bss7Bone structure and strength QTL 76.4femur strength trait (VT:0010010)femur midshaft polar moment of inertia (CMO:0001669)1575788062101769107Rat
70155Gcs1Gastric cancer susceptibility QTL13.8stomach morphology trait (VT:0000470)stomach tumor susceptibility score (CMO:0002043)1576306099101769107Rat
1300118Bp190Blood pressure QTL 1902.94arterial blood pressure trait (VT:2000000)blood pressure measurement (CMO:0000003)158226252098288169Rat
1300120Kidm7Kidney mass QTL 73.55kidney mass (VT:0002707)left kidney wet weight to body weight ratio (CMO:0001954)158226252098288169Rat
1581519Cm59Cardiac mass QTL 592.80.05heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)158885347095840528Rat

Markers in Region
D15Rat60  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_5.015106,884,632 - 106,884,806NCBIRnor5.0
RGSC_v3.415103,126,417 - 103,126,618RGDRGSC3.4
RGSC_v3.415103,126,418 - 103,126,618UniSTSRGSC3.4
RGSC_v3.115103,142,198 - 103,142,398RGD
RH 3.4 Map15651.4UniSTS
RH 3.4 Map15651.4RGD
RH 2.0 Map15560.0RGD
SHRSP x BN Map1560.7698RGD
Cytogenetic Map15q24UniSTS


Expression


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 reproductive system respiratory system appendage
High
Medium 18
Low 2 56 4 2
Below cutoff 3 9 6 4 2 4 1 1 11 7 1

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000090448
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl15103,440,212 - 103,441,030 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000095295   ⟹   ENSRNOP00000076878
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1595,292,265 - 95,296,091 (-)Ensembl
RefSeq Acc Id: NM_001402362   ⟹   NP_001389291
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr815101,699,580 - 101,703,175 (-)NCBI
mRatBN7.21595,292,429 - 95,296,024 (-)NCBI
Protein Sequences
Protein RefSeqs NP_001389291 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein BBD13390 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000076878
  ENSRNOP00000076878.1
Reference Protein Sequences
RefSeq Acc Id: ENSRNOP00000076878   ⟸   ENSRNOT00000095295
RefSeq Acc Id: NP_001389291   ⟸   NM_001402362
- UniProtKB: A0A679AYI7 (UniProtKB/TrEMBL)
Protein Domains
HMG box

Transcriptome

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


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1304724 AgrOrtholog
BioCyc Gene G2FUF-12450 BioCyc
Ensembl Genes ENSRNOG00000052579 Ensembl
  ENSRNOG00000063983 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000095295 ENTREZGENE
  ENSRNOT00000095295.1 UniProtKB/TrEMBL
Gene3D-CATH 1.10.30.10 UniProtKB/TrEMBL
InterPro HMG_box_dom UniProtKB/TrEMBL
  HMG_box_dom_sf UniProtKB/TrEMBL
  SOX_fam UniProtKB/TrEMBL
NCBI Gene 306168 ENTREZGENE
PANTHER SOX TRANSCRIPTION FACTOR UniProtKB/TrEMBL
  TRANSCRIPTION FACTOR SOX-21 UniProtKB/TrEMBL
Pfam HMG_box UniProtKB/TrEMBL
  SOXp UniProtKB/TrEMBL
PhenoGen Sox21 PhenoGen
PROSITE HMG_BOX_2 UniProtKB/TrEMBL
RatGTEx ENSRNOG00000052579 RatGTEx
  ENSRNOG00000063983 RatGTEx
SMART HMG UniProtKB/TrEMBL
Superfamily-SCOP SSF47095 UniProtKB/TrEMBL
UniProt A0A679AYI7 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2022-06-02 Sox21  SRY-box transcription factor 21  Sox21  SRY-box transcription factor 21  Data merged from RGD:149736497 737654 PROVISIONAL
2021-08-09 Sox21  SRY-box transcription factor 21      Symbol and Name status set to provisional 45752 PROVISIONAL
2019-08-05 Sox21  SRY-box transcription factor 21  Sox21  SRY box 21  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2015-11-12 Sox21  SRY box 21  Sox21  SRY (sex determining region Y)-box 21  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-09-18 Sox21  SRY (sex determining region Y)-box 21  Sox21  SRY-box containing gene 21   Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-04-30 Sox21  SRY-box containing gene 21   Sox21_predicted  SRY-box containing gene 21 (predicted)  'predicted' is removed 2292626 APPROVED
2005-01-12 Sox21_predicted  SRY-box containing gene 21 (predicted)      Symbol and Name status set to approved 70820 APPROVED