Tcf23 (transcription factor 23) - Rat Genome Database

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Gene: Tcf23 (transcription factor 23) Rattus norvegicus
Analyze
Symbol: Tcf23
Name: transcription factor 23
RGD ID: 1586500
Description: Predicted to enable several functions, including DNA-binding transcription factor activity, RNA polymerase II-specific; RNA polymerase II transcription regulatory region sequence-specific DNA binding activity; and transcription regulator inhibitor activity. Predicted to be involved in developmental process; negative regulation of muscle cell differentiation; and negative regulation of transcription by RNA polymerase II. Predicted to act upstream of or within decidualization and positive regulation of gene expression. Predicted to be located in euchromatin. Orthologous to human TCF23 (transcription factor 23); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; bis(2-ethylhexyl) phthalate; bisphenol A.
Type: protein-coding
RefSeq Status: MODEL
Previously known as: LOC688600; rCG61335-like; similar to transcription factor 23
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2625,397,889 - 25,406,639 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl625,397,937 - 25,405,880 (-)EnsemblmRatBN7.2 Ensembl
Rnor_6.0626,763,159 - 26,772,074 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl626,762,761 - 26,771,164 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0636,578,788 - 36,586,815 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4625,384,001 - 25,388,552 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera624,888,605 - 24,897,506 (-)NCBICelera
Cytogenetic Map6q14NCBI
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
euchromatin  (ISO)

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. GOA pipeline RGD automated data pipeline
3. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:24571987  


Genomics

Comparative Map Data
Tcf23
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2625,397,889 - 25,406,639 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl625,397,937 - 25,405,880 (-)EnsemblmRatBN7.2 Ensembl
Rnor_6.0626,763,159 - 26,772,074 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl626,762,761 - 26,771,164 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0636,578,788 - 36,586,815 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4625,384,001 - 25,388,552 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera624,888,605 - 24,897,506 (-)NCBICelera
Cytogenetic Map6q14NCBI
TCF23
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38227,149,004 - 27,156,974 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 Ensembl227,149,004 - 27,156,974 (+)EnsemblGRCh38hg38GRCh38
GRCh37227,371,872 - 27,379,842 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36227,225,506 - 27,229,239 (+)NCBINCBI36Build 36hg18NCBI36
Celera227,218,248 - 27,222,122 (+)NCBICelera
Cytogenetic Map2p23.3NCBI
HuRef227,113,796 - 27,117,670 (+)NCBIHuRef
CHM1_1227,301,867 - 27,305,741 (+)NCBICHM1_1
T2T-CHM13v2.0227,190,651 - 27,198,626 (+)NCBIT2T-CHM13v2.0
Tcf23
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39531,125,946 - 31,145,406 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl531,126,006 - 31,134,362 (+)EnsemblGRCm39 Ensembl
GRCm38530,968,602 - 30,988,062 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl530,968,662 - 30,977,018 (+)EnsemblGRCm38mm10GRCm38
MGSCv37531,271,050 - 31,279,391 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36531,245,258 - 31,253,599 (+)NCBIMGSCv36mm8
Celera528,448,052 - 28,456,393 (+)NCBICelera
Cytogenetic Map5B1NCBI
Tcf23
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554699,123,987 - 9,127,633 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554699,123,987 - 9,130,728 (+)NCBIChiLan1.0ChiLan1.0
TCF23
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.12A27,237,282 - 27,241,149 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl2A27,237,282 - 27,241,149 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v02A27,148,122 - 27,152,006 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
TCF23
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11721,139,408 - 21,145,014 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1721,140,794 - 21,144,053 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1721,032,667 - 21,037,060 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.01721,461,572 - 21,465,965 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl1721,461,740 - 21,464,999 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.11721,148,277 - 21,152,683 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.01721,159,382 - 21,163,788 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.01721,206,240 - 21,210,647 (+)NCBIUU_Cfam_GSD_1.0
Tcf23
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440629265,441,223 - 65,447,315 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049364935,395,283 - 5,398,141 (-)EnsemblSpeTri2.0
SpeTri2.0NW_0049364935,395,222 - 5,398,141 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
TCF23
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl3111,976,845 - 111,983,790 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.13111,976,848 - 111,983,879 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.23118,975,334 - 118,982,436 (-)NCBISscrofa10.2Sscrofa10.2susScr3
TCF23
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11480,459,590 - 80,466,272 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl1480,461,732 - 80,465,499 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366604531,675,387 - 31,681,683 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Tcf23
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046247389,256,670 - 9,263,332 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046247389,256,432 - 9,262,894 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Tcf23
45 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:28
Count of miRNA genes:28
Interacting mature miRNAs:28
Transcripts:ENSRNOT00000009090
Prediction methods:Miranda, Rnahybrid
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
738023Alc17Alcohol consumption QTL 173.10.003consumption behavior trait (VT:0002069)ethanol drink intake rate to body weight ratio (CMO:0001616)6127574569Rat
1354616Despr12Despair related QTL 120.0012locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)6127574569Rat
1549905Stresp10Stress response QTL 106.830.0066stress-related behavior trait (VT:0010451)number of approaches toward negative stimulus before onset of defensive burying response (CMO:0001960)6127574569Rat
2300176Bmd51Bone mineral density QTL 5111.70.0001femur mineral mass (VT:0010011)bone mineral density (CMO:0001226)6127574569Rat
2300190Bmd52Bone mineral density QTL 5211.20.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)6127574569Rat
1331743Uae28Urinary albumin excretion QTL 284.5urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)6134235784Rat
1578758Tcas9Tongue tumor susceptibility QTL 93.29tongue integrity trait (VT:0010553)number of squamous cell tumors of the tongue with diameter greater than 3 mm (CMO:0001950)6137618905Rat
1598843Cm63Cardiac mass QTL 632.6heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)6139036266Rat
7411603Foco13Food consumption QTL 135.50.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)6141223769Rat
8552962Pigfal16Plasma insulin-like growth factor 1 level QTL 169.4blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)6141223769Rat
7411542Bw127Body weight QTL 1275.50.001body mass (VT:0001259)body weight gain (CMO:0000420)6141223769Rat
9589129Insul24Insulin level QTL 2419.060.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)6141223769Rat
9589048Scfw3Subcutaneous fat weight QTL 34.570.001subcutaneous adipose mass (VT:1000472)abdominal subcutaneous fat pad weight (CMO:0002069)6141223769Rat
2293709Bss23Bone structure and strength QTL 235.180.0001femur morphology trait (VT:0000559)femur cross-sectional area (CMO:0001661)6142487980Rat
2293650Bss31Bone structure and strength QTL 315.050.0001femur strength trait (VT:0010010)femur midshaft polar moment of inertia (CMO:0001669)6142487980Rat
2293656Bss28Bone structure and strength QTL 286.790.0001femur morphology trait (VT:0000559)femur midshaft cortical cross-sectional area (CMO:0001663)6142487980Rat
7411584Foco4Food consumption QTL 44.30.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)6142838846Rat
738024Sach5Saccharine consumption QTL 53.90.00039consumption behavior trait (VT:0002069)saccharin intake volume to total fluid intake volume ratio (CMO:0001601)6143394190Rat
2301972Bp325Blood pressure QTL 3254.8arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)6172227641Rat
1300128Rf16Renal function QTL 163.89renal blood flow trait (VT:2000006)absolute change in renal blood flow rate (CMO:0001168)6507449734434305Rat
1300164Rf15Renal function QTL 153.12renal blood flow trait (VT:2000006)absolute change in renal blood flow rate (CMO:0001168)6507449754641141Rat
4145119Mcs25Mammary carcinoma susceptibility QTL 250.0001mammary gland integrity trait (VT:0010552)ratio of deaths to total study population during a period of time (CMO:0001023)610894415110548006Rat
1578665Bss16Bone structure and strength QTL 164.4femur morphology trait (VT:0000559)bone trabecular cross-sectional area (CMO:0002311)61173566972593685Rat
1578668Bmd14Bone mineral density QTL 143.8femur mineral mass (VT:0010011)total volumetric bone mineral density (CMO:0001728)61173566972593685Rat
10401812Kidm54Kidney mass QTL 54kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)61436878859368788Rat
10401800Kidm49Kidney mass QTL 49kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)61436878859368788Rat
1576309Emca7Estrogen-induced mammary cancer QTL 74mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)615107216107351382Rat
1359023Bp272Blood pressure QTL 2722.5arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)61653614027261739Rat
2292589Emca10Estrogen-induced mammary cancer QTL 100.048mammary gland integrity trait (VT:0010552)post-insult time to mammary tumor formation (CMO:0000345)61653614061536140Rat
1354664Slep2Serum leptin concentration QTL 24.49blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)61653614071636405Rat
1641898Colcr4Colorectal carcinoma resistance QTL43.710.0007intestine integrity trait (VT:0010554)well differentiated malignant colorectal tumor surface area measurement (CMO:0002077)62033877762613667Rat
2293839Kiddil2Kidney dilation QTL 24.8kidney pelvis morphology trait (VT:0004194)hydronephrosis severity score (CMO:0001208)62086642281133036Rat
2293841Kiddil4Kidney dilation QTL 44.4kidney pelvis morphology trait (VT:0004194)hydronephrosis severity score (CMO:0001208)62086642281133036Rat


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
Low 3 20 28 12 19 12 8 11 13 26 14 11 8
Below cutoff 23 29 29 29 53 9 4

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000009090   ⟹   ENSRNOP00000009090
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl625,397,937 - 25,405,880 (-)Ensembl
Rnor_6.0 Ensembl626,762,761 - 26,771,164 (-)Ensembl
RefSeq Acc Id: XM_001067558   ⟹   XP_001067558
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2625,397,889 - 25,406,639 (-)NCBI
Rnor_6.0626,763,159 - 26,772,063 (-)NCBI
Rnor_5.0636,578,788 - 36,586,815 (-)NCBI
RGSC_v3.4625,384,001 - 25,388,552 (-)RGD
Sequence:
Protein Sequences
Protein RefSeqs XP_001067558 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDM02954 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: XP_001067558   ⟸   XM_001067558
- UniProtKB: D4A6W7 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000009090   ⟸   ENSRNOT00000009090
Protein Domains
bHLH

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D4A6W7-F1-model_v2 AlphaFold D4A6W7 1-215 view protein structure

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:1586500 AgrOrtholog
BioCyc Gene G2FUF-38339 BioCyc
Ensembl Genes ENSRNOG00000025736 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000009090 ENTREZGENE
  ENSRNOP00000009090.5 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000009090 ENTREZGENE
  ENSRNOT00000009090.6 UniProtKB/TrEMBL
Gene3D-CATH 4.10.280.10 UniProtKB/TrEMBL
InterPro HLH_DNA-bd UniProtKB/TrEMBL
  HLH_DNA-bd_sf UniProtKB/TrEMBL
KEGG Report rno:688600 UniProtKB/TrEMBL
NCBI Gene 688600 ENTREZGENE
Pfam HLH UniProtKB/TrEMBL
PhenoGen Tcf23 PhenoGen
PROSITE HLH UniProtKB/TrEMBL
SMART HLH UniProtKB/TrEMBL
Superfamily-SCOP HLH_basic UniProtKB/TrEMBL
UniProt D4A6W7 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2013-05-24 Tcf23  transcription factor 23  LOC100364945  rCG61335-like  Data Merged 1643240 APPROVED
2010-05-05 LOC100364945  rCG61335-like      Symbol and Name status set to provisional 70820 PROVISIONAL
2010-03-09 Tcf23  transcription factor 23  LOC688600  similar to transcription factor 23  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-01-09 LOC688600  similar to transcription factor 23  LOC684101  similar to transcription factor 23  Data Merged 1643240 APPROVED
2006-11-20 LOC684101  similar to transcription factor 23      Symbol and Name status set to provisional 70820 PROVISIONAL
2006-11-19 LOC688600  similar to transcription factor 23      Symbol and Name status set to provisional 70820 PROVISIONAL