Tcf21 (transcription factor 21) - Rat Genome Database

Name: Tcf21
Creator: Rat Genome Database
License: Creative Commons CC BY 4.0
Keywords: Rat Gene RGD Genome

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Gene: Tcf21 (transcription factor 21) Rattus norvegicus

Analyze

Symbol:

Tcf21

Name:

transcription factor 21

RGD ID:

620523

Description:

Predicted to enable several functions, including DNA-binding transcription factor activity, RNA polymerase II-specific; DNA-binding transcription factor binding activity; and E-box binding activity. Involved in Sertoli cell differentiation; embryonic digestive tract morphogenesis; and gland development. Predicted to be located in nucleoplasm. Predicted to be part of transcription regulator complex. Orthologous to human TCF21 (transcription factor 21); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 2,3,7,8-Tetrachlorodibenzofuran; 4-tert-Octylphenol.

Type:

protein-coding

RefSeq Status:

PROVISIONAL

Previously known as:

Capsulin; MGC112908; Msf-1; Pod1

RGD Orthologs

Human

Mouse

Chinchilla

Bonobo

Dog

Squirrel

Pig

Green Monkey

Naked Mole-Rat

Alliance Genes

More Info

more info ...

More Info

Species	Gene symbol and name	Data Source	Assertion derived from	less info ...
Orthologs ¹				less info ...
Homo sapiens (human):	TCF21 (transcription factor 21)	HGNC	EggNOG, Ensembl, HomoloGene, Inparanoid, NCBI, OMA, OrthoDB, OrthoMCL, Panther, PhylomeDB, Treefam
Mus musculus (house mouse):	Tcf21 (transcription factor 21)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chinchilla lanigera (long-tailed chinchilla):	Tcf21 (transcription factor 21)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Pan paniscus (bonobo/pygmy chimpanzee):	TCF21 (transcription factor 21)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Canis lupus familiaris (dog):	TCF21 (transcription factor 21)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Ictidomys tridecemlineatus (thirteen-lined ground squirrel):	Tcf21 (transcription factor 21)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Sus scrofa (pig):	TCF21 (transcription factor 21)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chlorocebus sabaeus (green monkey):	TCF21 (transcription factor 21)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Heterocephalus glaber (naked mole-rat):	Tcf21 (transcription factor 21)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Alliance orthologs ³
Homo sapiens (human):	TCF21 (transcription factor 21)	Alliance	DIOPT (Ensembl Compara\|HGNC\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Mus musculus (house mouse):	Tcf21 (transcription factor 21)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Danio rerio (zebrafish):	tcf21 (transcription factor 21)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Drosophila melanogaster (fruit fly):	HLH54F	Alliance	DIOPT (OrthoFinder\|OrthoInspector\|PANTHER\|SonicParanoid)
Xenopus tropicalis (tropical clawed frog):	tcf21	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|SonicParanoid)

Latest Assembly:

mRatBN7.2 - mRatBN7.2 Assembly

Position:

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
mRatBN7.2	1	22,701,353 - 22,704,212 (+)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	1	22,701,353 - 22,704,202 (+)	Ensembl		mRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx	1	22,480,305 - 22,483,164 (+)	NCBI	Rnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.0	1	28,480,090 - 28,482,949 (+)	NCBI	Rnor_SHRSP
UTH_Rnor_WKY_Bbb_1.0	1	22,677,349 - 22,680,208 (+)	NCBI	Rnor_WKY
Rnor_6.0	1	23,906,717 - 23,909,576 (+)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	1	23,906,717 - 23,909,566 (+)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	1	25,370,183 - 25,373,042 (+)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	1	23,211,054 - 23,213,913 (+)	NCBI	RGSC3.4	RGSC_v3.4	rn4	RGSC3.4
RGSC_v3.1	1	23,214,112 - 23,214,625 (+)	NCBI
Celera	1	21,429,543 - 21,432,402 (+)	NCBI		Celera
Cytogenetic Map	1	p12	NCBI

JBrowse:

View Region in Genome Browser (JBrowse)

Model

Annotation Click to see Annotation Detail View

Disease Annotations Click to see Annotation Detail View

coronary artery disease (ISO)

genetic disease (ISO)

Paroxysmal Atrial Fibrillation (ISO)

ventricular septal defect (ISO)

Gene-Chemical Interaction Annotations Click to see Annotation Detail View

(1->4)-beta-D-glucan (ISO)

1,1-dichloroethene (ISO)

17beta-estradiol (ISO)

2,3,7,8-tetrachlorodibenzodioxine (EXP,ISO)

2,3,7,8-Tetrachlorodibenzofuran (EXP)

3-isobutyl-1-methyl-7H-xanthine (ISO)

4,4'-sulfonyldiphenol (ISO)

4-hydroxyphenyl retinamide (ISO)

4-tert-Octylphenol (EXP)

8-Br-cAMP (ISO)

acrylamide (EXP)

aflatoxin B1 (ISO)

all-trans-retinoic acid (ISO)

ammonium chloride (EXP)

amphetamine (EXP)

antirheumatic drug (ISO)

arsenite(3-) (ISO)

barium sulfate (EXP)

benzo[a]pyrene (ISO)

bis(2-ethylhexyl) phthalate (EXP)

bisphenol A (EXP,ISO)

bisphenol F (ISO)

Butylbenzyl phthalate (EXP)

carbon nanotube (ISO)

carmustine (ISO)

CGP 52608 (ISO)

choline (ISO)

cobalt atom (ISO)

corticosterone (EXP)

cytarabine (ISO)

dexamethasone (ISO)

dibutyl phthalate (EXP,ISO)

diethylstilbestrol (EXP,ISO)

dioxygen (ISO)

dipentyl phthalate (EXP)

doxorubicin (ISO)

endosulfan (EXP)

entinostat (ISO)

fenthion (ISO)

folic acid (ISO)

genistein (ISO)

gentamycin (EXP)

hydrogen cyanide (ISO)

kojic acid (ISO)

L-methionine (ISO)

Licarin A (ISO)

methotrexate (ISO)

methylmercury chloride (ISO)

mifepristone (EXP)

N-methyl-4-phenylpyridinium (EXP)

N-nitrosodiethylamine (ISO)

ozone (ISO)

p-tert-Amylphenol (EXP)

paracetamol (EXP)

perfluorooctane-1-sulfonic acid (ISO)

phenobarbital (ISO)

potassium cyanide (ISO)

potassium dichromate (ISO)

propanal (ISO)

propiconazole (ISO)

resveratrol (ISO)

rotenone (ISO)

sulforaphane (ISO)

tamoxifen (ISO)

tetrachloromethane (ISO)

titanium dioxide (ISO)

trichloroethene (EXP)

valproic acid (ISO)

vinclozolin (EXP)

vitamin E (ISO)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

animal organ morphogenesis (ISO)

branching involved in ureteric bud morphogenesis (ISO,ISS)

branchiomeric skeletal muscle development (ISO,ISS)

bronchiole development (ISO,ISS)

developmental process (IBA)

diaphragm development (ISO,ISS)

embryonic digestive tract morphogenesis (IMP)

epithelial cell differentiation (ISO,ISS)

gland development (IMP)

glomerulus development (ISO,ISS)

kidney development (ISO)

lung alveolus development (ISO,ISS)

lung morphogenesis (ISO,ISS)

lung vasculature development (ISO,ISS)

metanephric glomerular capillary formation (ISO,ISS)

metanephric mesenchymal cell differentiation (ISO,ISS)

morphogenesis of a branching structure (ISO,ISS)

negative regulation of androgen receptor signaling pathway (ISO,ISS)

negative regulation of transcription by RNA polymerase II (ISO,ISS)

positive regulation of transcription by RNA polymerase II (ISO,ISS)

regulation of transcription by RNA polymerase II (IBA)

reproductive structure development (ISO,ISS)

respiratory system development (ISO,ISS)

roof of mouth development (ISO,ISS)

Sertoli cell differentiation (IDA)

sex determination (ISO,ISS)

sex differentiation (ISO)

spleen development (ISO,ISS)

ureteric bud development (ISO,ISS)

vasculature development (ISO,ISS)

Cellular Component

nucleoplasm (IEA,ISO)

nucleus (ISO,ISS)

transcription regulator complex (ISO)

Molecular Function

bHLH transcription factor binding (ISO)

DNA-binding transcription activator activity, RNA polymerase II-specific (ISO,ISS)

DNA-binding transcription factor activity, RNA polymerase II-specific (IBA)

DNA-binding transcription repressor activity, RNA polymerase II-specific (ISO,ISS)

E-box binding (ISO,ISS)

histone deacetylase binding (ISO)

nuclear androgen receptor binding (ISO)

protein binding (ISO)

protein dimerization activity (IEA)

RNA polymerase II transcription regulatory region sequence-specific DNA binding (IBA)

sequence-specific double-stranded DNA binding (ISO)

References

References - curated

#	Reference Title	Reference Citation
1.	The role of capsulin in the morphogenesis and differentiation of fetal rat gastric mucosa.	Andersson M, etal., Int J Dev Biol 2001 Dec;45(8):887-93.
2.	MiRNA-Related Polymorphisms in miR-146a and TCF21 Are Associated with Increased Susceptibility to Coronary Artery Disease in an Iranian Population.	Bastami M, etal., Genet Test Mol Biomarkers. 2016 May;20(5):241-8. doi: 10.1089/gtmb.2015.0253. Epub 2016 Feb 24.
3.	Basic helix-loop-helix transcription factor TCF21 is a downstream target of the male sex determining gene SRY.	Bhandari RK, etal., PLoS One. 2011;6(5):e19935. doi: 10.1371/journal.pone.0019935. Epub 2011 May 17.
4.	Disrupted gonadogenesis and male-to-female sex reversal in Pod1 knockout mice.	Cui S, etal., Development. 2004 Aug;131(16):4095-105.
5.	Identification of the rat homologue of the mouse capsulin gene by cDNA representational difference analysis.	Familari M and Giraud AS, Gene 1998 Nov 19;222(2):245-8.
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.	Modulation of the expression and transactivation of androgen receptor by the basic helix-loop-helix transcription factor Pod-1 through recruitment of histone deacetylase 1.	Hong CY, etal., Mol Endocrinol. 2005 Sep;19(9):2245-57. Epub 2005 May 26.
8.	Capsulin: a novel bHLH transcription factor expressed in epicardial progenitors and mesenchyme of visceral organs.	Lu J, etal., Mech Dev. 1998 Apr;73(1):23-32.
9.	Rat ISS GO annotations from MGI mouse gene data--August 2006	MGD data from the GO Consortium
10.	Electronic Transfer of LocusLink and RefSeq Data	NCBI rat LocusLink and RefSeq merged data July 26, 2002
11.	The basic-helix-loop-helix protein pod1 is critically important for kidney and lung organogenesis.	Quaggin SE, etal., Development. 1999 Dec;126(24):5771-83.
12.	GOA pipeline	RGD automated data pipeline
13.	Data Import for Chemical-Gene Interactions	RGD automated import pipeline for gene-chemical interactions
14.	TCF21 rs12190287 Polymorphisms Are Associated with Ventricular Septal Defects in a Chinese Population.	Yang L, etal., Genet Test Mol Biomarkers. 2017 May;21(5):312-315. doi: 10.1089/gtmb.2016.0324. Epub 2017 Mar 27.
15.	Association Between TCF21 Gene Polymorphism with the Incidence of Paroxysmal Atrial Fibrillation and the Efficacy of Radiofrequency Ablation for Patients with Paroxysmal Atrial Fibrillation.	Zhang X, etal., Int J Gen Med. 2022 May 16;15:4975-4983. doi: 10.2147/IJGM.S366956. eCollection 2022.

Additional References at PubMed

PMID:9507058	PMID:9545526	PMID:10944221	PMID:11287187	PMID:12477932	PMID:12493738	PMID:12493912	PMID:12619136	PMID:23034159	PMID:32661376

Genomics

Comparative Map Data

Tcf21
(Rattus norvegicus - Norway rat)

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
mRatBN7.2	1	22,701,353 - 22,704,212 (+)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	1	22,701,353 - 22,704,202 (+)	Ensembl		mRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx	1	22,480,305 - 22,483,164 (+)	NCBI	Rnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.0	1	28,480,090 - 28,482,949 (+)	NCBI	Rnor_SHRSP
UTH_Rnor_WKY_Bbb_1.0	1	22,677,349 - 22,680,208 (+)	NCBI	Rnor_WKY
Rnor_6.0	1	23,906,717 - 23,909,576 (+)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	1	23,906,717 - 23,909,566 (+)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	1	25,370,183 - 25,373,042 (+)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	1	23,211,054 - 23,213,913 (+)	NCBI	RGSC3.4	RGSC_v3.4	rn4	RGSC3.4
RGSC_v3.1	1	23,214,112 - 23,214,625 (+)	NCBI
Celera	1	21,429,543 - 21,432,402 (+)	NCBI		Celera
Cytogenetic Map	1	p12	NCBI

TCF21
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38	6	133,889,113 - 133,895,537 (+)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh38.p13 Ensembl	6	133,889,113 - 133,895,553 (+)	Ensembl	GRCh38		hg38	GRCh38
GRCh37	6	134,210,251 - 134,216,675 (+)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	6	134,251,970 - 134,258,368 (+)	NCBI	NCBI36	Build 36	hg18	NCBI36
Build 34	6	134,251,969 - 134,258,368	NCBI
Celera	6	134,951,327 - 134,957,746 (+)	NCBI		Celera
Cytogenetic Map	6	q23.2	NCBI
HuRef	6	131,779,608 - 131,786,028 (+)	NCBI		HuRef
CHM1_1	6	134,473,121 - 134,479,537 (+)	NCBI		CHM1_1
T2T-CHM13v2.0	6	135,077,847 - 135,084,271 (+)	NCBI		T2T-CHM13v2.0

Tcf21
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	10	22,693,162 - 22,696,042 (-)	NCBI	GRCm39	GRCm39	mm39
GRCm39 Ensembl	10	22,693,180 - 22,696,073 (-)	Ensembl		GRCm39 Ensembl
GRCm38	10	22,817,263 - 22,820,143 (-)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	10	22,817,281 - 22,820,174 (-)	Ensembl	GRCm38		mm10	GRCm38
MGSCv37	10	22,537,069 - 22,539,934 (-)	NCBI	GRCm37	MGSCv37	mm9	NCBIm37
MGSCv36	10	22,506,679 - 22,509,544 (-)	NCBI		MGSCv36	mm8
Celera	10	23,754,029 - 23,756,913 (-)	NCBI		Celera
Cytogenetic Map	10	A3	NCBI
cM Map	10	10.33	NCBI

Tcf21
(Chinchilla lanigera - long-tailed chinchilla)

Chinchilla Assembly	Chr	Position (strand)	Source	Genome Browsers
Chinchilla Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
ChiLan1.0 Ensembl	NW_004955439	2,617,492 - 2,620,644 (-)	Ensembl	ChiLan1.0
ChiLan1.0	NW_004955439	2,617,562 - 2,620,613 (-)	NCBI	ChiLan1.0	ChiLan1.0

TCF21
(Pan paniscus - bonobo/pygmy chimpanzee)

Bonobo Assembly	Chr	Position (strand)	Source	Genome Browsers
Bonobo Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
NHGRI_mPanPan1	6	151,768,855 - 151,772,401 (+)	NCBI		NHGRI_mPanPan1
Mhudiblu_PPA_v0	6	131,656,582 - 131,662,983 (+)	NCBI	Mhudiblu_PPA_v0	Mhudiblu_PPA_v0	panPan3
PanPan1.1	6	135,754,896 - 135,761,294 (+)	NCBI	panpan1.1	PanPan1.1	panPan2
PanPan1.1 Ensembl	6	135,754,896 - 135,761,294 (+)	Ensembl	panpan1.1		panPan2

TCF21
(Canis lupus familiaris - dog)

Dog Assembly	Chr	Position (strand)	Source	Genome Browsers
Dog Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
CanFam3.1	1	26,856,281 - 26,859,654 (+)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1
CanFam3.1 Ensembl	1	26,856,587 - 26,859,647 (+)	Ensembl	CanFam3.1		canFam3	CanFam3.1
Dog10K_Boxer_Tasha	1	27,737,867 - 27,741,067 (+)	NCBI		Dog10K_Boxer_Tasha
ROS_Cfam_1.0	1	27,014,669 - 27,017,873 (+)	NCBI		ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl	1	27,015,081 - 27,017,857 (+)	Ensembl		ROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1	1	26,898,755 - 26,901,959 (+)	NCBI		UMICH_Zoey_3.1
UNSW_CanFamBas_1.0	1	26,778,392 - 26,781,591 (+)	NCBI		UNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0	1	27,087,943 - 27,091,143 (+)	NCBI		UU_Cfam_GSD_1.0

Tcf21
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)

Squirrel Assembly	Chr	Position (strand)	Source	Genome Browsers
Squirrel Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
HiC_Itri_2	NW_024404946	121,954,674 - 121,957,679 (+)	NCBI		HiC_Itri_2
SpeTri2.0 Ensembl	NW_004936560	1,733,903 - 1,736,890 (+)	Ensembl	SpeTri2.0
SpeTri2.0	NW_004936560	1,733,903 - 1,736,895 (+)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

TCF21
(Sus scrofa - pig)

Pig Assembly	Chr	Position (strand)	Source	Genome Browsers
Pig Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Sscrofa11.1 Ensembl	1	29,975,280 - 29,978,255 (-)	Ensembl	Sscrofa11.1		susScr11	Sscrofa11.1
Sscrofa11.1	1	29,975,280 - 29,978,273 (-)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1
Sscrofa10.2	1	33,477,834 - 33,478,622 (-)	NCBI	Sscrofa10.2	Sscrofa10.2	susScr3

TCF21
(Chlorocebus sabaeus - green monkey)

Green Monkey Assembly	Chr	Position (strand)	Source	Genome Browsers
Green Monkey Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
ChlSab1.1	13	39,607,179 - 39,610,336 (-)	NCBI	ChlSab1.1	ChlSab1.1	chlSab2
ChlSab1.1 Ensembl	13	39,607,182 - 39,610,388 (-)	Ensembl	ChlSab1.1	ChlSab1.1 Ensembl	chlSab2
Vero_WHO_p1.0	NW_023666040	11,792,052 - 11,795,253 (-)	NCBI	Vero_WHO_p1.0	Vero_WHO_p1.0

Tcf21
(Heterocephalus glaber - naked mole-rat)

Naked Mole-Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Naked Mole-Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
HetGla_female_1.0 Ensembl	NW_004624942	890,365 - 893,811 (-)	Ensembl	HetGla_female_1.0	HetGla_female_1.0 Ensembl	hetGla2
HetGla 1.0	NW_004624942	890,465 - 893,679 (-)	NCBI	HetGla_female_1.0	HetGla 1.0	hetGla2

Variants

Variants in Tcf21
9 total Variants

miRNA Target Status

Predicted Target Of

	Summary Value
Count of predictions:	75
Count of miRNA genes:	56
Interacting mature miRNAs:	70
Transcripts:	ENSRNOT00000022798
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 (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.

RGD ID	Symbol	Name	LOD	P Value	Trait	Sub Trait	Chr	Start	Stop	Species
1354647	Despr8	Despair related QTL 8		0.0000341	locomotor behavior trait (VT:0001392)	amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)	1	1	24744506	Rat
2298546	Neuinf4	Neuroinflammation QTL 4	5.1		nervous system integrity trait (VT:0010566)	spinal cord RT1-B protein level (CMO:0002132)	1	1	28736750	Rat
2313053	Bss51	Bone structure and strength QTL 51	3.8	0.0001	tibia length (VT:0004357)	tibia length (CMO:0000450)	1	1	32356093	Rat
2313070	Bss52	Bone structure and strength QTL 52	4.4	0.0001	body length (VT:0001256)	body length (CMO:0000013)	1	1	32356093	Rat
2313090	Bmd69	Bone mineral density QTL 69	4.4	0.0001	tibia mineral mass (VT:1000283)	compact volumetric bone mineral density (CMO:0001730)	1	1	32356093	Rat
738020	Pia8	Pristane induced arthritis QTL 8	4.7		joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	1	1	65833076	Rat
1578650	Bmd6	Bone mineral density QTL 6	12.2		femur mineral mass (VT:0010011)	total volumetric bone mineral density (CMO:0001728)	1	509108	43284926	Rat
1578651	Bmd7	Bone mineral density QTL 7	14.2		femur mineral mass (VT:0010011)	compact volumetric bone mineral density (CMO:0001730)	1	509108	43284926	Rat
1578669	Bss9	Bone structure and strength QTL 9	6.3		femur morphology trait (VT:0000559)	bone trabecular cross-sectional area (CMO:0002311)	1	509108	43284926	Rat
1554320	Bmd1	Bone mineral density QTL 1	12.2	0.0001	femur mineral mass (VT:0010011)	volumetric bone mineral density (CMO:0001553)	1	509108	86060548	Rat
1600360	Mcs16	Mammary carcinoma susceptibility QTL 16	2.4		mammary gland integrity trait (VT:0010552)	mammary tumor number (CMO:0000343)	1	2244390	43433040	Rat
7421626	Bp360	Blood pressure QTL 360		0.001	arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	1	4393289	49393289	Rat
631688	Hcas2	Hepatocarcinoma susceptibility QTL 2	3	0.0001	liver integrity trait (VT:0010547)	liver tumorous lesion number (CMO:0001068)	1	5925874	115540829	Rat
4889451	Eae29	Experimental allergic encephalomyelitis QTL 29	5.51		nervous system integrity trait (VT:0010566)	experimental autoimmune encephalomyelitis severity score (CMO:0001419)	1	5925877	24697545	Rat
631508	Sald1	Serum aldosterone level QTL 1	3.7		blood aldosterone amount (VT:0005346)	serum aldosterone level (CMO:0000487)	1	9856001	54856001	Rat
2302038	Pia31	Pristane induced arthritis QTL 31	5.5	0.001	blood autoantibody amount (VT:0003725)	serum immunoglobulin M-type rheumatoid factor level relative to an arbitrary reference serum (CMO:0002111)	1	10992065	55992065	Rat
1300167	Hrtrt2	Heart rate QTL 2	4.35		heart pumping trait (VT:2000009)	heart rate (CMO:0000002)	1	11481312	75088344	Rat
2313062	Bmd73	Bone mineral density QTL 73	3.9	0.0001	tibia mineral mass (VT:1000283)	compact volumetric bone mineral density (CMO:0001730)	1	11481312	82174945	Rat
2313065	Bss67	Bone structure and strength QTL 67	3.1	0.0001	tibia area (VT:1000281)	tibia total energy absorbed before break (CMO:0001736)	1	11481312	82174945	Rat
2313069	Bss68	Bone structure and strength QTL 68	2.9	0.0001	tibia size trait (VT:0100001)	tibia total energy absorbed before break (CMO:0001736)	1	11481312	82174945	Rat
2313075	Bss66	Bone structure and strength QTL 66	3.4	0.0001	tibia length (VT:0004357)	tibia length (CMO:0000450)	1	11481312	82174945	Rat
2313077	Bss69	Bone structure and strength QTL 69	3.5	0.0001	tibia strength trait (VT:1000284)	bone polar moment of inertia (CMO:0001558)	1	11481312	82174945	Rat
2313092	Bmd72	Bone mineral density QTL 72	2.5	0.0001	tibia mineral mass (VT:1000283)	total volumetric bone mineral density (CMO:0001728)	1	11481312	82174945	Rat
2313097	Bss70	Bone structure and strength QTL 70	3.5	0.0001	tibia strength trait (VT:1000284)	tibia total energy absorbed before break (CMO:0001736)	1	11481312	82174945	Rat
2317755	Glom22	Glomerulus QTL 22	3.8		urine protein amount (VT:0005160)	urine protein level (CMO:0000591)	1	11481482	32355910	Rat
1578756	Iddm22	Insulin dependent diabetes mellitus QTL 22	2.7		blood glucose amount (VT:0000188)	blood glucose level (CMO:0000046)	1	11835181	56835181	Rat
5684998	Bss101	Bone structure and strength QTL 101	3.6		tibia strength trait (VT:1000284)	tibia ultimate force (CMO:0001734)	1	15431621	49361612	Rat
5684999	Bss102	Bone structure and strength QTL 102	5.5	0.00000072	tibia strength trait (VT:1000284)	tibia stiffness (CMO:0001735)	1	15431621	49361612	Rat
631494	Bp95	Blood pressure QTL 95	40	0.0001	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	1	16206210	49268520	Rat
634353	Rends2	Renal damage susceptibility QTL 2		0.05	kidney blood vessel morphology trait (VT:0000530)	organ lesion measurement (CMO:0000677)	1	19333571	56983283	Rat
1558642	Prcr2	Prostate cancer resistance QTL 2	4.3		prostate integrity trait (VT:0010571)	area of ventral prostate occupied by tumorous lesions to total ventral prostate area ratio (CMO:0000899)	1	20763158	44095856	Rat
724520	Bp145	Blood pressure QTL 145	2.1	0.0024	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	1	20784828	65784828	Rat
1357397	Bw41	Body weight QTL 41	4.19	0.0001	body mass (VT:0001259)	body weight (CMO:0000012)	1	22340647	49361612	Rat
1357401	Bw43	Body weight QTL 43	3.75		body mass (VT:0001259)	body weight (CMO:0000012)	1	22340647	49361612	Rat
1357400	Bw62	Body weight QTL62	4.05		inguinal fat pad mass (VT:0010424)	inguinal fat pad weight to body weight ratio (CMO:0001253)	1	22340647	67340647	Rat
631495	Bp96	Blood pressure QTL 96	4.52		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	1	22340647	102268831	Rat

Markers in Region

Tcf21

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	1	22,701,607 - 22,701,731 (+)	MAPPER	mRatBN7.2
Rnor_6.0	1	23,906,972 - 23,907,095	NCBI	Rnor6.0
Rnor_5.0	1	25,370,438 - 25,370,561	UniSTS	Rnor5.0
RGSC_v3.4	1	23,211,309 - 23,211,432	UniSTS	RGSC3.4
Celera	1	21,429,798 - 21,429,921	UniSTS
Cytogenetic Map	1	p12	UniSTS

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	3	36	10	10	11	10				35	33	11
Low		7	39	31		31			4		8
Below cutoff			7		7		6	7	54				6

View RNA-SEQ Expression Data

Sequence

Nucleotide Sequences


RefSeq Transcripts	NM_001032397	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	AF061752	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	BC100106	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	CH474002	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	JACYVU010000008	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

Reference Sequences

RefSeq Acc Id:

ENSRNOT00000022798 ⟹ ENSRNOP00000022798

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2 Ensembl	1	22,701,353 - 22,704,202 (+)	Ensembl
Rnor_6.0 Ensembl	1	23,906,717 - 23,909,566 (+)	Ensembl

RefSeq Acc Id:

NM_001032397 ⟹ NP_001027569

RefSeq Status:

PROVISIONAL

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	1	22,701,353 - 22,704,212 (+)	NCBI
Rnor_6.0	1	23,906,717 - 23,909,576 (+)	NCBI
Rnor_5.0	1	25,370,183 - 25,373,042 (+)	NCBI
RGSC_v3.4	1	23,211,054 - 23,213,913 (+)	RGD
Celera	1	21,429,543 - 21,432,402 (+)	RGD

Sequence:

show sequence

GTTAAGGCCAGGACTCCAGGGGTGGGGAGATAAAGCTCTAGTTTCCCTGTCGCGGGAATCCTTT
TGGTCGTTTTCACAACTCTGTGAAGGGGAAGCTGTGAGACAAGGCTGCCAGATCCCATCTGGAA
ACCCAACACACAGAAGTGGCAACTCCGTACTTTAGAGACCCTTTCATTTCCGTTTCGGTGTCTC
TCTCTCTCTCCCTCCTCCACCTCCTCTCTAAACATGTCCACTGGCTCCCTCAGCGATGTAGAAG
ACCTTCAAGAGGTGGAGATGCTGGACTGTGACTCCCTGAAAGTGGATTCCAACAAGGAGTTTGG
AACTTCCAATGAGAGCACCGAGGAGGGTTCCAACTGCGAGAACGGGTCTCCACAGAAGGGTCGT
GGTGGCCTGGGCAAGAGGAGGAAGGCGCCCACCAAGAAAAGCCCGCTGAGCGGGGTCAGCCAGG
AGGGCAAGCAGGTCCAGCGCAACGCGGCCAATGCACGCGAGCGGGCCCGCATGCGGGTGCTGAG
CAAGGCCTTCTCCAGGCTCAAGACTACCCTTCCCTGGGTGCCCCCGGACACCAAGCTCTCCAAG
CTGGACACTCTCAGGCTGGCGTCCAGCTACATCGCGCACCTGAGGCAGATCCTGGCCAACGACA
AGTACGAGAATGGTTACATTCACCCAGTCAACCTGACTTGGCCCTTTATGGTGGCCGGCAAACC
TGAGAGTGACCTAAAGGAAGTGGTGACCGCGAGCCGCTTGTGTGGAACCACCGCATCCTGACCT
TGGAGGTGTGAGTCTGGGAACCCTGCGCTCTCGAGGGCAGTGGGCCGGTGAGGGTGACGACCCC
TGCCCTCCCCTCCCCGTCTCTGCTGCCGCCTTGCATCGCTCCTCTCCCTATCCCACCCCGCAAG
AACACTTAACTGCGACGAGGAGATTCGTTTCCAAACCGAAGGAGACCAACTGTACTTACAGATT
CCCATCTATTTAACTTGATTAACTTCTGCCCTGAATGACTGTGAGCCTGGCTGGTCCAAGTGCA
ATATGTAATTATATATAGTATATATAAATAGATAATAAGAGCCTATCAATGTGTATCTTTTGTA
CAATATGTTGTAAAATGTAGATCATAGAATAGCTGACTTTGACAGTCACATTTATAAAATAAAT
CACTCAAAGAAATATATTTTTTTCAAACAGGTTTTGCTATTTCCGAAAATAAATCTTTCTTTAT
ATTGCTAAAAAAAAAAAAAAAAAAAAAAA

hide sequence

Protein Sequences


Protein RefSeqs	NP_001027569	(Get FASTA)	NCBI Sequence Viewer
GenBank Protein	AAD03823	(Get FASTA)	NCBI Sequence Viewer
	AAI00107	(Get FASTA)	NCBI Sequence Viewer
	EDL87735	(Get FASTA)	NCBI Sequence Viewer
	EDL87736	(Get FASTA)	NCBI Sequence Viewer

Reference Sequences

RefSeq Acc Id:	NP_001027569 ⟸ NM_001032397
- UniProtKB:	Q498R2 (UniProtKB/TrEMBL)
- Sequence:	show sequence MSTGSLSDVEDLQEVEMLDCDSLKVDSNKEFGTSNESTEEGSNCENGSPQKGRGGLGKRRKAPT KKSPLSGVSQEGKQVQRNAANARERARMRVLSKAFSRLKTTLPWVPPDTKLSKLDTLRLASSYI AHLRQILANDKYENGYIHPVNLTWPFMVAGKPESDLKEVVTASRLCGTTAS hide sequence

RefSeq Acc Id:

ENSRNOP00000022798 ⟸ ENSRNOT00000022798

Protein Domains

bHLH

Protein Structures

Name	Modeler	Protein Id	AA Range	Protein Structure
AF-Q498R2-F1-model_v2	AlphaFold	Q498R2	1-179	view protein structure

Transcriptome

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

Promoters

RGD ID:

13689534

Promoter ID:

EPDNEW_R59

Type:

single initiation site

Name:

Tcf21_1

Description:

transcription factor 21

SO ACC ID:

SO:0000170

Source:

EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)

Experiment Methods:

Single-end sequencing.

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0	1	23,906,699 - 23,906,759	EPDNEW

Additional Information

External Database Links

Database	Acc Id	Source(s)
AGR Gene	RGD:620523	AgrOrtholog
BioCyc Gene	G2FUF-62047	BioCyc
Ensembl Genes	ENSRNOG00000016700	Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein	ENSRNOP00000022798	ENTREZGENE
	ENSRNOP00000022798.4	UniProtKB/TrEMBL
Ensembl Transcript	ENSRNOT00000022798	ENTREZGENE
	ENSRNOT00000022798.6	UniProtKB/TrEMBL
Gene3D-CATH	4.10.280.10	UniProtKB/TrEMBL
IMAGE_CLONE	IMAGE:7379660	IMAGE-MGC_LOAD
InterPro	HLH_DNA-bd_sf	UniProtKB/TrEMBL
	HLH_DNA_bd	UniProtKB/TrEMBL
KEGG Report	rno:252856	UniProtKB/TrEMBL
MGC_CLONE	MGC:112908	IMAGE-MGC_LOAD
NCBI Gene	252856	ENTREZGENE
PANTHER	BASIC HELIX-LOOP-HELIX TRANSCRIPTION FACTOR, TWIST	UniProtKB/TrEMBL
	TRANSCRIPTION FACTOR 21	UniProtKB/TrEMBL
Pfam	HLH	UniProtKB/TrEMBL
PhenoGen	Tcf21	PhenoGen
PROSITE	HLH	UniProtKB/TrEMBL
SMART	HLH	UniProtKB/TrEMBL
Superfamily-SCOP	HLH_basic	UniProtKB/TrEMBL
UniProt	Q498R2	ENTREZGENE, UniProtKB/TrEMBL

Nomenclature History

Date	Current Symbol	Current Name	Previous Symbol	Previous Name	Description	Reference	Status
2004-09-10	Tcf21	transcription factor 21			Symbol and Name status set to approved	1299863	APPROVED
2002-08-07	Tcf21	transcription factor 21			Symbol and Name status set to provisional	70820	PROVISIONAL

Gene Annotator (Functional Annotation) unavailable	Gene Annotator (Annotation Distribution) unavailable	Variant Visualizer (Genomic Variants) unavailble Variant Visualizer (Genomic Variants) unavailable
Gene Annotator (Functional Annotation)	Gene Annotator (Annotation Distribution)	Variant Visualizer (Genomic Variants)

InterViewer (Protein-Protein Interactions) unavailable	Gviewer (Genome Viewer) unavailable	Variant Visualizer (Damaging Variants) unavailble Variant Visualizer (Damaging Variants) unavailable
InterViewer (Protein-Protein Interactions)	GViewer (Genome Viewer)	Variant Visualizer (Damaging Variants)

Gene Annotator (Annotation Comparison) unavailable	OLGA (Gene List Generator) unavailable
Gene Annotator (Annotation Comparison)	OLGA (Gene List Generator)	Excel (Download)

MOET (Multi-Ontology Enrichement) unavailable	GOLF (Gene-Ortholog Location Finder) unavailable
MOET (Multi-Ontology Enrichement)	GOLF (Gene-Ortholog Location Finder)

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