Sox7 (SRY-box transcription factor 7) - Rat Genome Database

Send us a Message



Submit Data |  Help |  Video Tutorials |  News |  Publications |  Download |  REST API |  Citing RGD |  Contact   
Gene: Sox7 (SRY-box transcription factor 7) Rattus norvegicus
Analyze
Symbol: Sox7
Name: SRY-box transcription factor 7
RGD ID: 1310038
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 several processes, including endoderm formation; regulation of DNA-templated transcription; and regulation of canonical Wnt signaling pathway. Predicted to act upstream of or within positive regulation of DNA-templated transcription and regulation of transcription by RNA polymerase II. Predicted to be located in cytoplasm. Predicted to be active in nucleus. Orthologous to human SOX7 (SRY-box transcription factor 7); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 6-propyl-2-thiouracil; amitrole.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: LOC290317; SRY (sex determining region Y)-box 7; SRY box 7; SRY-box containing gene 7; transcription factor SOX-7
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
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
GRCr81542,356,405 - 42,363,166 (+)NCBIGRCr8
mRatBN7.21538,180,503 - 38,187,264 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1538,180,503 - 38,187,264 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1540,037,796 - 40,044,594 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01541,188,477 - 41,195,275 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01539,641,092 - 39,647,853 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01547,293,699 - 47,300,460 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1547,293,699 - 47,300,460 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01551,053,093 - 51,059,854 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41543,207,965 - 43,214,726 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11543,223,666 - 43,228,547 (+)NCBI
Celera1537,862,141 - 37,868,902 (+)NCBICelera
Cytogenetic Map15p12NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

References

References - curated
# Reference Title Reference Citation
1. 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.
2. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
3. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
4. Comprehensive gene review and curation RGD comprehensive gene curation
Additional References at PubMed
PMID:10320775   PMID:15082719   PMID:15220343   PMID:18682240   PMID:18819930   PMID:19108950   PMID:19328208   PMID:19515696   PMID:21146513   PMID:25847511   PMID:30871773  


Genomics

Comparative Map Data
Sox7
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81542,356,405 - 42,363,166 (+)NCBIGRCr8
mRatBN7.21538,180,503 - 38,187,264 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1538,180,503 - 38,187,264 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1540,037,796 - 40,044,594 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01541,188,477 - 41,195,275 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01539,641,092 - 39,647,853 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01547,293,699 - 47,300,460 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1547,293,699 - 47,300,460 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01551,053,093 - 51,059,854 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41543,207,965 - 43,214,726 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11543,223,666 - 43,228,547 (+)NCBI
Celera1537,862,141 - 37,868,902 (+)NCBICelera
Cytogenetic Map15p12NCBI
SOX7
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38810,723,768 - 10,730,511 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl810,723,768 - 10,730,511 (-)EnsemblGRCh38hg38GRCh38
GRCh37810,581,278 - 10,588,021 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36810,618,688 - 10,625,432 (-)NCBINCBI36Build 36hg18NCBI36
Build 34810,618,688 - 10,625,432NCBI
Celera89,709,191 - 9,716,191 (-)NCBICelera
Cytogenetic Map8p23.1NCBI
HuRef89,511,594 - 9,518,400 (-)NCBIHuRef
CHM1_1810,646,800 - 10,653,606 (-)NCBICHM1_1
T2T-CHM13v2.089,008,562 - 9,015,305 (+)NCBIT2T-CHM13v2.0
Sox7
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391464,181,155 - 64,188,181 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1464,181,122 - 64,188,181 (+)EnsemblGRCm39 Ensembl
GRCm381463,943,706 - 63,950,732 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1463,943,673 - 63,950,732 (+)EnsemblGRCm38mm10GRCm38
MGSCv371464,562,543 - 64,569,569 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361462,897,816 - 62,904,842 (+)NCBIMGSCv36mm8
Celera1461,720,720 - 61,727,748 (+)NCBICelera
Cytogenetic Map14D1NCBI
cM Map1433.34NCBI
Sox7
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495540352,253,482 - 52,259,884 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495540352,253,816 - 52,259,884 (-)NCBIChiLan1.0ChiLan1.0
SOX7
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2727,180,826 - 27,187,703 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan183,213,289 - 3,220,167 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v088,476,357 - 8,483,144 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
SOX7
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12527,216,111 - 27,222,142 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2527,215,528 - 27,220,227 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2527,871,952 - 27,889,698 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.02527,370,450 - 27,388,195 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl2527,370,562 - 27,377,493 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.12527,324,552 - 27,342,303 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.02527,218,744 - 27,236,487 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.02527,372,604 - 27,390,369 (+)NCBIUU_Cfam_GSD_1.0
Sox7
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_0244049435,963,679 - 5,970,072 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049366752,616,077 - 2,622,436 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049366752,616,086 - 2,622,436 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SOX7
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1413,938,388 - 13,945,166 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11413,938,381 - 13,945,324 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21415,286,380 - 15,293,330 (-)NCBISscrofa10.2Sscrofa10.2susScr3
SOX7
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.188,368,632 - 8,375,529 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl88,368,912 - 8,375,530 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366605234,052,909 - 34,059,785 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Sox7
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462475824,556,010 - 24,562,213 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462475824,556,436 - 24,562,204 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Sox7
24 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:1015
Count of miRNA genes:327
Interacting mature miRNAs:436
Transcripts:ENSRNOT00000016503
Prediction methods:Microtar, Miranda, Targetscan
Result types:miRGate_prediction

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

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
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
731170Pur3Proteinuria QTL 32.30.0005urine protein amount (VT:0005160)urine protein excretion rate (CMO:0000759)15141686771Rat
1641887Alcrsp14Alcohol response QTL 14response to alcohol trait (VT:0010489)brain neurotensin receptor 1 density (CMO:0002068)15142356671Rat
2298549Neuinf12Neuroinflammation QTL 123.5nervous system integrity trait (VT:0010566)spinal cord beta-2 microglobulin mRNA level (CMO:0002125)15155302115Rat
10401805Kidm51Kidney mass QTL 51kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)1530632945306329Rat
738017Hcas7Hepatocarcinoma susceptibility QTL 72.91liver integrity trait (VT:0010547)liver nonremodeling tumorous lesion volume to total liver volume ratio (CMO:0001464)15226636846921453Rat
1582251Gluco24Glucose level QTL 243.20.0008blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)15553075650530756Rat
631273Lecl2Lens clarity QTL 20.001lens clarity trait (VT:0001304)age of onset/diagnosis of cataract (CMO:0001584)151059608955596089Rat
2300167Bmd63Bone mineral density QTL 635.90.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)151111114256111142Rat
2300173Bmd62Bone mineral density QTL 6212.80.0001lumbar vertebra mineral mass (VT:0010511)volumetric bone mineral density (CMO:0001553)151111114256111142Rat
2293688Bss29Bone structure and strength QTL 295.310.0001femur morphology trait (VT:0000559)femur midshaft cortical cross-sectional area (CMO:0001663)151111114256111142Rat
2317750Glom26Glomerulus QTL 264.3urine protein amount (VT:0005160)urine protein level (CMO:0000591)151249614165205939Rat
61424Scl1Serum cholesterol level QTL 17.70.001blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)151672552880672115Rat
1331729Rf42Renal function QTL 423.071kidney blood vessel physiology trait (VT:0100012)absolute change in renal blood flow rate (CMO:0001168)151736289773690657Rat
2324620Coatc3Coat color QTL 3coat/hair pigmentation trait (VT:0010463)pigmented coat/hair area to total coat/hair area ratio (CMO:0001810)151985656646187442Rat
10054130Srcrt8Stress Responsive Cort QTL 82.180.0085blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)152211793367117933Rat
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
1582214Stl21Serum triglyceride level QTL 213.10.022blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)152803066582262678Rat
1582227Gluco30Glucose level QTL 303.60.0003blood glucose amount (VT:0000188)absolute change in blood glucose level area under curve (CMO:0002034)152803066582262678Rat
1582228Epfw3Epididymal fat weight QTL 34.10.0002epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)152803066582262678Rat
1582242Gluco28Glucose level QTL 283.30.0008blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)152803066582262678Rat
1582244Bw79Body weight QTL 7940.0002epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)152803066582262678Rat
2293691Bmd37Bone mineral density QTL 376.60.0001femur strength trait (VT:0010010)femur total energy absorbed before break (CMO:0001677)153361105871477291Rat
2293686Bmd36Bone mineral density QTL 367.40.0001femur strength trait (VT:0010010)femoral neck ultimate force (CMO:0001703)153361105871477291Rat
1598828Glom14Glomerulus QTL 142.5kidney glomerulus morphology trait (VT:0005325)index of glomerular damage (CMO:0001135)153405413979054139Rat

Markers in Region
RH131053  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21538,186,946 - 38,187,127 (+)MAPPERmRatBN7.2
Rnor_6.01547,300,143 - 47,300,323NCBIRnor6.0
Rnor_5.01551,059,537 - 51,059,717UniSTSRnor5.0
RGSC_v3.41543,214,409 - 43,214,589UniSTSRGSC3.4
Celera1537,868,585 - 37,868,765UniSTS
RH 3.4 Map15282.4UniSTS
Cytogenetic Map15p12UniSTS


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 renal system reproductive system respiratory system appendage
High
Medium 23 8 14 11
Low 3 20 52 36 19 36 8 11 74 27 22 8
Below cutoff 5 5 5 5

Sequence


RefSeq Acc Id: ENSRNOT00000016503   ⟹   ENSRNOP00000016503
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1538,180,503 - 38,187,264 (+)Ensembl
Rnor_6.0 Ensembl1547,293,699 - 47,300,460 (+)Ensembl
RefSeq Acc Id: NM_001106045   ⟹   NP_001099515
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81542,356,405 - 42,363,166 (+)NCBI
mRatBN7.21538,180,503 - 38,187,264 (+)NCBI
Rnor_6.01547,293,699 - 47,300,460 (+)NCBI
Rnor_5.01551,053,093 - 51,059,854 (+)NCBI
RGSC_v3.41543,207,965 - 43,214,726 (+)RGD
Celera1537,862,141 - 37,868,902 (+)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_001099515 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDL85328 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000016503
  ENSRNOP00000016503.4
RefSeq Acc Id: NP_001099515   ⟸   NM_001106045
- UniProtKB: D3ZTE1 (UniProtKB/TrEMBL),   A6K6G8 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000016503   ⟸   ENSRNOT00000016503
Protein Domains
HMG box   Sox C-terminal

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D3ZTE1-F1-model_v2 AlphaFold D3ZTE1 1-383 view protein structure

Transcriptome

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

Promoters
RGD ID:13699782
Promoter ID:EPDNEW_R10304
Type:single initiation site
Name:Sox7_1
Description:SRY box 7
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01547,293,697 - 47,293,757EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1310038 AgrOrtholog
BioCyc Gene G2FUF-13394 BioCyc
Ensembl Genes ENSRNOG00000012049 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000016503 ENTREZGENE
  ENSRNOT00000016503.5 UniProtKB/TrEMBL
Gene3D-CATH 1.10.30.10 UniProtKB/TrEMBL
InterPro DUF3547 UniProtKB/TrEMBL
  HMG_box_dom_sf UniProtKB/TrEMBL
  HMG_superfamily UniProtKB/TrEMBL
  Sox7/17/18_central UniProtKB/TrEMBL
KEGG Report rno:290317 UniProtKB/TrEMBL
NCBI Gene 290317 ENTREZGENE
PANTHER SOX TRANSCRIPTION FACTOR UniProtKB/TrEMBL
  TRANSCRIPTION FACTOR SOX-7 UniProtKB/TrEMBL
Pfam HMG_box UniProtKB/TrEMBL
  Sox_C_TAD UniProtKB/TrEMBL
PhenoGen Sox7 PhenoGen
PROSITE HMG_BOX_2 UniProtKB/TrEMBL
  SOX_C UniProtKB/TrEMBL
RatGTEx ENSRNOG00000012049 RatGTEx
SMART HMG UniProtKB/TrEMBL
Superfamily-SCOP HMG-box UniProtKB/TrEMBL
UniProt A6K6G8 ENTREZGENE, UniProtKB/TrEMBL
  D3ZTE1 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2019-08-07 Sox7  SRY-box transcription factor 7  Sox7  SRY box 7  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2015-11-12 Sox7  SRY box 7  Sox7  SRY (sex determining region Y)-box 7  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-09-18 Sox7  SRY (sex determining region Y)-box 7  Sox7  SRY-box containing gene 7   Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-04-30 Sox7  SRY-box containing gene 7   Sox7_predicted  SRY-box containing gene 7 (predicted)  'predicted' is removed 2292626 APPROVED
2005-01-12 Sox7_predicted  SRY-box containing gene 7 (predicted)      Symbol and Name status set to approved 70820 APPROVED