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Gene: Hoxc13 (homeobox C13) Rattus norvegicus

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Symbol:

Hoxc13

Name:

homeobox C13

RGD ID:

1563984

Description:

Predicted to enable several functions, including DNA-binding transcription activator activity, RNA polymerase II-specific; RNA polymerase II cis-regulatory region sequence-specific DNA binding activity; and chromatin binding activity. Predicted to be involved in positive regulation of DNA-templated transcription and regulation of transcription by RNA polymerase II. Predicted to act upstream of or within several processes, including hair follicle development; nail development; and tongue morphogenesis. Predicted to be located in nucleus. Human ortholog(s) of this gene implicated in ectodermal dysplasia 9. Orthologous to human HOXC13 (homeobox C13); INTERACTS WITH alpha-Zearalanol; bisphenol A; copper atom.

Type:

protein-coding

RefSeq Status:

MODEL

Previously known as:

homeobox protein Hox-C13; LOC315337; RGD1563984; similar to homeodomain protein

RGD Orthologs

Alliance Orthologs

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):	HOXC13 (homeobox C13)	HGNC	EggNOG, Ensembl, HomoloGene, Inparanoid, NCBI, OMA, OrthoDB, OrthoMCL, Panther, PhylomeDB, Treefam
Mus musculus (house mouse):	Hoxc13 (homeobox C13)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chinchilla lanigera (long-tailed chinchilla):	Hoxc13 (homeobox C13)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Pan paniscus (bonobo/pygmy chimpanzee):	HOXC13 (homeobox C13)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Canis lupus familiaris (dog):	HOXC13 (homeobox C13)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Ictidomys tridecemlineatus (thirteen-lined ground squirrel):	Hoxc13 (homeobox C13)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Sus scrofa (pig):	HOXC13 (homeobox C13)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chlorocebus sabaeus (green monkey):	HOXC13 (homeobox C13)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Heterocephalus glaber (naked mole-rat):	Hoxc13 (homeobox C13)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Alliance orthologs ³
Homo sapiens (human):	HOXC13 (homeobox C13)	Alliance	DIOPT (Ensembl Compara\|HGNC\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Mus musculus (house mouse):	Hoxc13 (homeobox C13)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Danio rerio (zebrafish):	hoxc13a (homeobox C13a)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Danio rerio (zebrafish):	hoxc13b (homeobox C13b)	Alliance	DIOPT (Ensembl Compara\|OrthoInspector\|PANTHER\|PhylomeDB)
Xenopus tropicalis (tropical clawed frog):	hoxc13	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)

Latest Assembly:

GRCr8 - GRCr8 Assembly

Position:

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCr8	7	135,937,126 - 135,943,962 (+)	NCBI		GRCr8
mRatBN7.2	7	134,058,640 - 134,065,479 (+)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	7	134,058,640 - 134,064,800 (+)	Ensembl		mRatBN7.2 Ensembl
Rnor_6.0	7	144,531,814 - 144,538,298 (+)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	7	144,531,814 - 144,537,966 (+)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	7	142,323,171 - 142,329,323 (+)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	7	141,685,004 - 141,691,159 (+)	NCBI	RGSC3.4	RGSC_v3.4	rn4	RGSC3.4
Celera	7	130,489,719 - 130,491,373 (+)	NCBI		Celera
Cytogenetic Map	7	q36	NCBI

JBrowse:

View Region in Genome Browser (JBrowse)

Model

Object Symbol	Species	Term	Qualifier	Evidence	With	Reference	Notes	Source	Original Reference(s)
Hoxc13	Rat	ectodermal dysplasia 9		ISO	RGD:1349214	8554872	ClinVar Annotator: match by term: Ectodermal dysplasia 9, hair/nail type	ClinVar	PMID:23063621\|PMID:23315978\|PMID:25741868
Hoxc13	Rat	Neurodevelopmental Disorders		ISO	RGD:1349214	8554872	ClinVar Annotator: match by term: Neurodevelopmental disorder	ClinVar	PMID:25741868

Object Symbol	Species	Term	Qualifier	Evidence	With	Reference	Notes	Source	Original Reference(s)
Hoxc13	Rat	BILATERAL CLEFT LIP		ISO	RGD:14101462	9068941	Ectodermal dysplasia-9	OMIA	PMID:28011715

Object Symbol	Species	Term	Qualifier	Evidence	With	Reference	Notes	Source	Original Reference(s)
Hoxc13	Rat	ectodermal dysplasia 9		ISO	RGD:1349214	7240710		OMIM

Only show annotations with direct experimental evidence (0 objects hidden)

Object Symbol	Species	Term	Qualifier	Evidence	With	Reference	Notes	Source	Original Reference(s)
Hoxc13	Rat	2,3,7,8-tetrachlorodibenzodioxine	affects expression	ISO	RGD:1557146	6480464	Tetrachlorodibenzodioxin affects the expression of HOXC13 mRNA	CTD	PMID:24058054
Hoxc13	Rat	2-palmitoylglycerol	increases expression	ISO	RGD:1349214	6480464	2-palmitoylglycerol results in increased expression of HOXC13 mRNA	CTD	PMID:37199045
Hoxc13	Rat	actinomycin D	multiple interactions	ISO	RGD:1349214	6480464	[Dactinomycin co-treated with nutlin 3] results in increased expression of HOXC13 mRNA	CTD	PMID:38460933
Hoxc13	Rat	afimoxifene	multiple interactions	ISO	RGD:1349214	6480464	afimoxifene inhibits the reaction [Estrogens results in decreased expression of HOXC13 mRNA]	CTD	PMID:21233418
Hoxc13	Rat	aflatoxin B1	decreases methylation	ISO	RGD:1349214	6480464	Aflatoxin B1 results in decreased methylation of HOXC13 gene	CTD	PMID:27153756
Hoxc13	Rat	alpha-Zearalanol	multiple interactions	EXP		6480464	[Zeranol co-treated with perfluorooctanoic acid] results in decreased expression of HOXC13 mRNA	CTD	PMID:35163327
Hoxc13	Rat	aristolochic acid A	increases expression	ISO	RGD:1349214	6480464	aristolochic acid I results in increased expression of HOXC13 mRNA	CTD	PMID:33212167
Hoxc13	Rat	arsane	multiple interactions	ISO	RGD:1349214	6480464	[sodium arsenite results in increased abundance of Arsenic] which results in decreased expression of HOXC13 more ...	CTD	PMID:39836092
Hoxc13	Rat	arsenic atom	multiple interactions	ISO	RGD:1349214	6480464	[sodium arsenite results in increased abundance of Arsenic] which results in decreased expression of HOXC13 more ...	CTD	PMID:39836092
Hoxc13	Rat	arsenite(3-)	increases methylation	ISO	RGD:1349214	6480464	arsenite results in increased methylation of HOXC13 promoter	CTD	PMID:23974009
Hoxc13	Rat	atrazine	increases expression	ISO	RGD:1349214	6480464	Atrazine results in increased expression of HOXC13 mRNA	CTD	PMID:22378314
Hoxc13	Rat	benzo[a]pyrene	decreases methylation	ISO	RGD:1349214	6480464	Benzo(a)pyrene results in decreased methylation of HOXC13 promoter	CTD	PMID:27901495
Hoxc13	Rat	benzo[a]pyrene	affects methylation	ISO	RGD:1349214	6480464	Benzo(a)pyrene affects the methylation of HOXC13 3' UTR	CTD	PMID:27901495
Hoxc13	Rat	bisphenol A	decreases expression	EXP		6480464	bisphenol A results in decreased expression of HOXC13 mRNA	CTD	PMID:25181051
Hoxc13	Rat	bisphenol A	affects methylation	ISO	RGD:1557146	6480464	bisphenol A affects the methylation of HOXC13 promoter	CTD	PMID:27334623
Hoxc13	Rat	cadmium dichloride	decreases expression	ISO	RGD:1349214	6480464	Cadmium Chloride results in decreased expression of HOXC13 mRNA	CTD	PMID:38568856
Hoxc13	Rat	camptothecin	increases expression	ISO	RGD:1349214	6480464	Camptothecin results in increased expression of HOXC13 mRNA	CTD	PMID:38460933
Hoxc13	Rat	CGP 52608	multiple interactions	ISO	RGD:1349214	6480464	CGP 52608 promotes the reaction [RORA protein binds to HOXC13 gene]	CTD	PMID:28238834
Hoxc13	Rat	cisplatin	increases expression	ISO	RGD:1349214	6480464	Cisplatin results in increased expression of HOXC13 mRNA	CTD	PMID:19561079\|PMID:27392435
Hoxc13	Rat	copper atom	increases expression	EXP		6480464	Copper deficiency results in increased expression of HOXC13 mRNA	CTD	PMID:26033743
Hoxc13	Rat	copper(0)	increases expression	EXP		6480464	Copper deficiency results in increased expression of HOXC13 mRNA	CTD	PMID:26033743
Hoxc13	Rat	coumestrol	decreases expression	ISO	RGD:1349214	6480464	Coumestrol results in decreased expression of HOXC13 mRNA	CTD	PMID:19167446
Hoxc13	Rat	dimethylselenide	multiple interactions	ISO	RGD:1349214	6480464	[[Hydroxyl Radical results in increased oxidation of dimethylselenide] which results in increased expression of HOXC13-AS more ...	CTD	PMID:33656867
Hoxc13	Rat	endosulfan	increases expression	ISO	RGD:1349214	6480464	Endosulfan results in increased expression of HOXC13 mRNA	CTD	PMID:26615145
Hoxc13	Rat	hydroxyl	multiple interactions	ISO	RGD:1349214	6480464	[[Hydroxyl Radical results in increased oxidation of dimethylselenide] which results in increased expression of HOXC13-AS more ...	CTD	PMID:33656867
Hoxc13	Rat	indole-3-methanol	affects expression	EXP		6480464	indole-3-carbinol affects the expression of HOXC13 mRNA	CTD	PMID:21396975
Hoxc13	Rat	nickel sulfate	increases expression	ISO	RGD:1349214	6480464	nickel sulfate results in increased expression of HOXC13 mRNA	CTD	PMID:22714537
Hoxc13	Rat	Nutlin-3	multiple interactions	ISO	RGD:1349214	6480464	[Dactinomycin co-treated with nutlin 3] results in increased expression of HOXC13 mRNA	CTD	PMID:38460933
Hoxc13	Rat	ozone	multiple interactions	ISO	RGD:1349214	6480464	[[Ozone results in increased oxidation of dimethylselenide] which results in increased expression of HOXC13-AS mRNA] more ...	CTD	PMID:33656867
Hoxc13	Rat	paracetamol	decreases expression	ISO	RGD:1349214	6480464	Acetaminophen results in decreased expression of HOXC13 mRNA	CTD	PMID:26690555
Hoxc13	Rat	perfluorooctanoic acid	multiple interactions	EXP		6480464	[Zeranol co-treated with perfluorooctanoic acid] results in decreased expression of HOXC13 mRNA	CTD	PMID:35163327
Hoxc13	Rat	sodium arsenite	affects expression	ISO	RGD:1349214	6480464	sodium arsenite affects the expression of HOXC13 mRNA	CTD	PMID:29319823
Hoxc13	Rat	sodium arsenite	decreases expression	ISO	RGD:1557146	6480464	sodium arsenite results in decreased expression of HOXC13 mRNA	CTD	PMID:36209798\|PMID:37682722
Hoxc13	Rat	sodium arsenite	multiple interactions	ISO	RGD:1349214	6480464	[sodium arsenite results in increased abundance of Arsenic] which results in decreased expression of HOXC13 more ...	CTD	PMID:39836092
Hoxc13	Rat	temozolomide	increases expression	ISO	RGD:1349214	6480464	Temozolomide results in increased expression of HOXC13 mRNA	CTD	PMID:31758290
Hoxc13	Rat	thapsigargin	decreases expression	ISO	RGD:1349214	6480464	Thapsigargin results in decreased expression of HOXC13 mRNA	CTD	PMID:29453283
Hoxc13	Rat	titanium dioxide	increases methylation	ISO	RGD:1557146	6480464	titanium dioxide results in increased methylation of HOXC13 gene	CTD	PMID:35295148
Hoxc13	Rat	titanium dioxide	increases expression	ISO	RGD:1557146	6480464	titanium dioxide results in increased expression of HOXC13 mRNA	CTD	PMID:35295148
Hoxc13	Rat	trichloroethene	increases expression	EXP		6480464	Trichloroethylene results in increased expression of HOXC13 mRNA	CTD	PMID:33387578
Hoxc13	Rat	tunicamycin	decreases expression	ISO	RGD:1349214	6480464	Tunicamycin results in decreased expression of HOXC13 mRNA	CTD	PMID:29453283
Hoxc13	Rat	valproic acid	affects expression	ISO	RGD:1557146	6480464	Valproic Acid affects the expression of HOXC13 mRNA	CTD	PMID:17292431
Hoxc13	Rat	valproic acid	increases expression	ISO	RGD:1349214	6480464	Valproic Acid results in increased expression of HOXC13 mRNA	CTD	PMID:23179753
Hoxc13	Rat	valproic acid	affects expression	ISO	RGD:1349214	6480464	Valproic Acid affects the expression of HOXC13 mRNA	CTD	PMID:25979313

Biological Process

Only show annotations with direct experimental evidence (0 objects hidden)

Object Symbol	Species	Term	Qualifier	Evidence	With	Reference	Notes	Source	Original Reference(s)
Hoxc13	Rat	anatomical structure morphogenesis	acts_upstream_of_or_within	ISO	RGD:1557146	1624291	MGI:1926422 PMID:9420327	RGD	PMID:9420327
Hoxc13	Rat	anatomical structure morphogenesis	acts_upstream_of_or_within	IEA	UniProtKB:P50207\|ensembl:ENSMUSP00000001700	1600115	GO_REF:0000107	Ensembl	GO_REF:0000107
Hoxc13	Rat	anterior/posterior pattern specification	acts_upstream_of_or_within	IEA	UniProtKB:P50207\|ensembl:ENSMUSP00000001700	1600115	GO_REF:0000107	Ensembl	GO_REF:0000107
Hoxc13	Rat	anterior/posterior pattern specification	acts_upstream_of_or_within	ISO	RGD:1557146	1624291	MGI:1926422 PMID:9420327	RGD	PMID:9420327
Hoxc13	Rat	hair follicle development	acts_upstream_of_or_within	ISO	RGD:1557146	1624291	MGI:1926422 PMID:21191399, PMID:9420327	RGD	PMID:21191399\|PMID:9420327
Hoxc13	Rat	hair follicle development	acts_upstream_of_or_within	IEA	UniProtKB:P50207\|ensembl:ENSMUSP00000001700	1600115	GO_REF:0000107	Ensembl	GO_REF:0000107
Hoxc13	Rat	nail development	acts_upstream_of_or_within	ISO	RGD:1557146	1624291	MGI:1926422 PMID:21191399	RGD	PMID:21191399
Hoxc13	Rat	nail development	acts_upstream_of_or_within	IEA	UniProtKB:P50207\|ensembl:ENSMUSP00000001700	1600115	GO_REF:0000107	Ensembl	GO_REF:0000107
Hoxc13	Rat	positive regulation of DNA-templated transcription	involved_in	ISO	RGD:1349214	1624291	UniProtKB:P17947 PMID:27506447	RGD	PMID:27506447
Hoxc13	Rat	positive regulation of DNA-templated transcription	involved_in	IEA	UniProtKB:P31276\|ensembl:ENSP00000243056	1600115	GO_REF:0000107	Ensembl	GO_REF:0000107
Hoxc13	Rat	positive regulation of transcription by RNA polymerase II	acts_upstream_of_or_within	ISO	RGD:1557146	1624291	PMID:21191399	RGD	PMID:21191399
Hoxc13	Rat	positive regulation of transcription by RNA polymerase II	acts_upstream_of_or_within	IEA	UniProtKB:P50207\|ensembl:ENSMUSP00000001700	1600115	GO_REF:0000107	Ensembl	GO_REF:0000107
Hoxc13	Rat	regulation of DNA-templated transcription	involved_in	IEA	InterPro:IPR017970	1600115	GO_REF:0000002	InterPro	GO_REF:0000002
Hoxc13	Rat	regulation of transcription by RNA polymerase II	involved_in	IBA	MGI:96173\|MGI:96205\|MGI:99560\|PANTHER:PTN008462040\|UniProtKB:P35453\|UniProtKB:Q92826\|ZFIN:ZDB-GENE-980526-365\|ZFIN:ZDB-GENE-990415-5	1600115	GO_REF:0000033	GO_Central	GO_REF:0000033
Hoxc13	Rat	tongue morphogenesis	acts_upstream_of_or_within	ISO	RGD:1557146	1624291	MGI:1926422 PMID:9420327	RGD	PMID:9420327
Hoxc13	Rat	tongue morphogenesis	acts_upstream_of_or_within	IEA	UniProtKB:P50207\|ensembl:ENSMUSP00000001700	1600115	GO_REF:0000107	Ensembl	GO_REF:0000107

Cellular Component

Only show annotations with direct experimental evidence (0 objects hidden)

Object Symbol	Species	Term	Qualifier	Evidence	With	Reference	Notes	Source	Original Reference(s)
Hoxc13	Rat	nucleus	located_in	ISO	RGD:1557146	1624291	PMID:21191399	RGD	PMID:21191399
Hoxc13	Rat	nucleus	located_in	IEA	UniProtKB:P50207\|ensembl:ENSMUSP00000001700	1600115	GO_REF:0000107	Ensembl	GO_REF:0000107
Hoxc13	Rat	nucleus	located_in	IEA	UniProtKB-KW:KW-0539	1600115	GO_REF:0000043	UniProt	GO_REF:0000043
Hoxc13	Rat	nucleus	located_in	IEA	UniRule:UR000401037	1600115	GO_REF:0000104	UniProt	GO_REF:0000104
Hoxc13	Rat	nucleus	located_in	IEA	UniProtKB-SubCell:SL-0191	1600115	GO_REF:0000044	UniProt	GO_REF:0000044

Molecular Function

Only show annotations with direct experimental evidence (0 objects hidden)

Object Symbol	Species	Term	Qualifier	Evidence	With	Reference	Notes	Source	Original Reference(s)
Hoxc13	Rat	chromatin binding	enables	ISO	RGD:1557146	1624291	PMID:21191399	RGD	PMID:21191399
Hoxc13	Rat	chromatin binding	enables	IEA	UniProtKB:P50207\|ensembl:ENSMUSP00000001700	1600115	GO_REF:0000107	Ensembl	GO_REF:0000107
Hoxc13	Rat	DNA binding	enables	IEA	UniRule:UR000401037	1600115	GO_REF:0000104	UniProt	GO_REF:0000104
Hoxc13	Rat	DNA binding	enables	IEA	InterPro:IPR001356	1600115	GO_REF:0000002	InterPro	GO_REF:0000002
Hoxc13	Rat	DNA binding	enables	IEA	UniProtKB-KW:KW-0238\|UniProtKB-KW:KW-0371	1600115	GO_REF:0000043	UniProt	GO_REF:0000043
Hoxc13	Rat	DNA-binding transcription activator activity, RNA polymerase II-specific	enables	ISO	RGD:1557146	1624291	PMID:21191399	RGD	PMID:21191399
Hoxc13	Rat	DNA-binding transcription activator activity, RNA polymerase II-specific	enables	IEA	UniProtKB:P50207\|ensembl:ENSMUSP00000001700	1600115	GO_REF:0000107	Ensembl	GO_REF:0000107
Hoxc13	Rat	DNA-binding transcription factor activity	enables	ISO	RGD:1349214	1624291	PMID:27506447	RGD	PMID:27506447
Hoxc13	Rat	DNA-binding transcription factor activity	enables	IEA	UniProtKB:P31276\|ensembl:ENSP00000243056	1600115	GO_REF:0000107	Ensembl	GO_REF:0000107
Hoxc13	Rat	DNA-binding transcription factor activity, RNA polymerase II-specific	enables	IBA	MGI:96173\|MGI:96205\|MGI:99560\|PANTHER:PTN008462040\|UniProtKB:P35453\|UniProtKB:Q92826\|ZFIN:ZDB-GENE-980526-365\|ZFIN:ZDB-GENE-990415-5	1600115	GO_REF:0000033	GO_Central	GO_REF:0000033
Hoxc13	Rat	DNA-binding transcription factor activity, RNA polymerase II-specific	enables	IEA	InterPro:IPR017970	1600115	GO_REF:0000002	InterPro	GO_REF:0000002
Hoxc13	Rat	DNA-binding transcription factor binding	enables	ISO	RGD:1349214	1624291	UniProtKB:P17947 PMID:27506447	RGD	PMID:27506447
Hoxc13	Rat	DNA-binding transcription factor binding	enables	IEA	UniProtKB:P31276\|ensembl:ENSP00000243056	1600115	GO_REF:0000107	Ensembl	GO_REF:0000107
Hoxc13	Rat	protein binding	enables	ISO	RGD:1349214	1624291	UniProtKB:O95644\|UniProtKB:P32519 PMID:18692240, PMID:25609649	RGD	PMID:18692240\|PMID:25609649
Hoxc13	Rat	RNA polymerase II cis-regulatory region sequence-specific DNA binding	enables	IBA	MGI:96173\|MGI:96205\|PANTHER:PTN008462040	1600115	GO_REF:0000033	GO_Central	GO_REF:0000033
Hoxc13	Rat	sequence-specific double-stranded DNA binding	enables	ISO	RGD:1349214	1624291	PMID:28473536	RGD	PMID:28473536
Hoxc13	Rat	sequence-specific double-stranded DNA binding	enables	IEA	UniProtKB:P31276\|ensembl:ENSP00000243056	1600115	GO_REF:0000107	Ensembl	GO_REF:0000107
Hoxc13	Rat	transcription cis-regulatory region binding	enables	ISO	RGD:1349214	1624291	PMID:27506447	RGD	PMID:27506447
Hoxc13	Rat	transcription cis-regulatory region binding	enables	IEA	UniProtKB:P31276\|ensembl:ENSP00000243056	1600115	GO_REF:0000107	Ensembl	GO_REF:0000107

#	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.	OMIM Disease Annotation Pipeline	OMIM Disease Annotation Pipeline
3.	GOA pipeline	RGD automated data pipeline
4.	ClinVar Automated Import and Annotation Pipeline	RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
5.	Data Import for Chemical-Gene Interactions	RGD automated import pipeline for gene-chemical interactions

PMID:9420327	PMID:21191399

Hoxc13
(Rattus norvegicus - Norway rat)

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCr8	7	135,937,126 - 135,943,962 (+)	NCBI		GRCr8
mRatBN7.2	7	134,058,640 - 134,065,479 (+)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	7	134,058,640 - 134,064,800 (+)	Ensembl		mRatBN7.2 Ensembl
Rnor_6.0	7	144,531,814 - 144,538,298 (+)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	7	144,531,814 - 144,537,966 (+)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	7	142,323,171 - 142,329,323 (+)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	7	141,685,004 - 141,691,159 (+)	NCBI	RGSC3.4	RGSC_v3.4	rn4	RGSC3.4
Celera	7	130,489,719 - 130,491,373 (+)	NCBI		Celera
Cytogenetic Map	7	q36	NCBI

HOXC13
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38	12	53,938,831 - 53,946,544 (+)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh38.p14 Ensembl	12	53,938,831 - 53,946,544 (+)	Ensembl	GRCh38		hg38	GRCh38
GRCh37	12	54,332,615 - 54,340,328 (+)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	12	52,618,843 - 52,626,595 (+)	NCBI	NCBI36	Build 36	hg18	NCBI36
Build 34	12	52,618,842 - 52,626,594	NCBI
Celera	12	53,982,194 - 53,989,933 (+)	NCBI		Celera
Cytogenetic Map	12	q13.13	NCBI
HuRef	12	51,370,279 - 51,377,685 (+)	NCBI		HuRef
CHM1_1	12	54,299,300 - 54,307,033 (+)	NCBI		CHM1_1
T2T-CHM13v2.0	12	53,904,353 - 53,912,048 (+)	NCBI		T2T-CHM13v2.0

Hoxc13
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	15	102,829,566 - 102,837,249 (+)	NCBI	GRCm39	GRCm39	mm39
GRCm39 Ensembl	15	102,829,538 - 102,837,249 (+)	Ensembl		GRCm39 Ensembl
GRCm38	15	102,921,131 - 102,928,814 (+)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	15	102,921,103 - 102,928,814 (+)	Ensembl	GRCm38		mm10	GRCm38
MGSCv37	15	102,751,562 - 102,759,245 (+)	NCBI	GRCm37	MGSCv37	mm9	NCBIm37
MGSCv36	15	102,749,165 - 102,756,848 (+)	NCBI		MGSCv36	mm8
Celera	15	105,078,954 - 105,086,637 (+)	NCBI		Celera
Cytogenetic Map	15	F3	NCBI
cM Map	15	57.99	NCBI

Hoxc13
(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_004955458	1,197,295 - 1,205,127 (+)	Ensembl	ChiLan1.0
ChiLan1.0	NW_004955458	1,197,295 - 1,205,098 (+)	NCBI	ChiLan1.0	ChiLan1.0

HOXC13
(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-v2	10	40,239,252 - 40,246,959 (-)	NCBI		NHGRI_mPanPan1-v2
NHGRI_mPanPan1	12	40,236,020 - 40,243,727 (-)	NCBI		NHGRI_mPanPan1
Mhudiblu_PPA_v0	12	34,808,575 - 34,816,324 (-)	NCBI	Mhudiblu_PPA_v0	Mhudiblu_PPA_v0	panPan3
PanPan1.1	12	35,596,821 - 35,604,560 (-)	NCBI	panpan1.1	PanPan1.1	panPan2
PanPan1.1 Ensembl	12	35,596,821 - 35,604,560 (-)	Ensembl	panpan1.1		panPan2

HOXC13
(Canis lupus familiaris - dog)

Dog Assembly	Chr	Position (strand)	Source	Genome Browsers
Dog Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
CanFam3.1	27	1,315,532 - 1,323,470 (-)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1
CanFam3.1 Ensembl	27	1,273,131 - 1,323,370 (-)	Ensembl	CanFam3.1		canFam3	CanFam3.1
Dog10K_Boxer_Tasha	27	44,926,178 - 44,934,051 (+)	NCBI		Dog10K_Boxer_Tasha
ROS_Cfam_1.0	27	1,319,256 - 1,327,126 (-)	NCBI		ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl	27	1,319,221 - 1,327,051 (-)	Ensembl		ROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1	27	1,336,900 - 1,344,764 (-)	NCBI		UMICH_Zoey_3.1
UNSW_CanFamBas_1.0	27	1,318,461 - 1,326,337 (-)	NCBI		UNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0	27	45,329,789 - 45,337,670 (+)	NCBI		UU_Cfam_GSD_1.0

Hoxc13
(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_024404945	61,997,436 - 62,004,487 (-)	NCBI		HiC_Itri_2
SpeTri2.0	NW_004936512	11,160,343 - 11,166,616 (+)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

HOXC13
(Sus scrofa - pig)

Pig Assembly	Chr	Position (strand)	Source	Genome Browsers
Pig Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Sscrofa11.1 Ensembl	5	19,151,084 - 19,158,646 (+)	Ensembl	Sscrofa11.1		susScr11	Sscrofa11.1
Sscrofa11.1	5	19,151,096 - 19,159,008 (+)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1
Sscrofa10.2	5	19,624,272 - 19,632,185 (+)	NCBI	Sscrofa10.2	Sscrofa10.2	susScr3

HOXC13
(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	11	50,039,034 - 50,057,178 (+)	NCBI	ChlSab1.1	ChlSab1.1	chlSab2
ChlSab1.1 Ensembl	11	50,049,509 - 50,055,895 (+)	Ensembl	ChlSab1.1	ChlSab1.1 Ensembl	chlSab2
Vero_WHO_p1.0	NW_023666037	195,985,021 - 195,992,836 (-)	NCBI	Vero_WHO_p1.0	Vero_WHO_p1.0

Hoxc13
(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_004624904	1,993,854 - 2,000,500 (+)	Ensembl	HetGla_female_1.0	HetGla_female_1.0 Ensembl	hetGla2
HetGla 1.0	NW_004624904	1,993,854 - 2,001,623 (+)	NCBI	HetGla_female_1.0	HetGla 1.0	hetGla2

Variants in Hoxc13
56 total Variants

Predicted Target Of

	Summary Value
Count of predictions:	85
Count of miRNA genes:	68
Interacting mature miRNAs:	72
Transcripts:	ENSRNOT00000033300
Prediction methods:	Microtar, 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.

The following QTLs overlap with this region.

RGD ID	Symbol	Name	LOD	P Value	Trait	Sub Trait	Chr	Start	Stop	Species
1300179	Kidm5	Kidney mass QTL 5	3.51		kidney mass (VT:0002707)	left kidney wet weight (CMO:0000083)	7	43747012	135012528	Rat
1354582	Stl11	Serum triglyceride level QTL 11	3.42		blood triglyceride amount (VT:0002644)	serum triglyceride level (CMO:0000360)	7	119513385	135012528	Rat
731176	Glom5	Glomerulus QTL 5	2.5	0.0035	kidney glomerulus morphology trait (VT:0005325)	count of superficial glomeruli not directly contacting the kidney surface (CMO:0001002)	7	96670164	135012528	Rat
1300112	Bp183	Blood pressure QTL 183	3.51		arterial blood pressure trait (VT:2000000)	blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)	7	111182207	135012528	Rat
1358914	Bp266	Blood pressure QTL 266			arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	7	83591953	134666232	Rat
2306821	Bp335	Blood pressure QTL 335		0.001	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	7	106571501	135012528	Rat
631663	Bw6	Body weight QTL 6	3.4		body mass (VT:0001259)	body weight (CMO:0000012)	7	111075573	134976056	Rat
2299163	Iddm34	Insulin dependent diabetes mellitus QTL 34	2.71		blood glucose amount (VT:0000188)	age at onset/diagnosis of type 1 diabetes mellitus (CMO:0001140)	7	91281130	135012528	Rat
70173	Niddm19	Non-insulin dependent diabetes mellitus QTL 19	4.33	0.00005	blood glucose amount (VT:0000188)	blood glucose level area under curve (AUC) (CMO:0000350)	7	64002457	135012528	Rat
1549899	Stresp8	Stress response QTL 8	4.37	0.0008	stress-related behavior trait (VT:0010451)	defensive burying duration (CMO:0001961)	7	90482196	135012528	Rat
731174	Uae23	Urinary albumin excretion QTL 23	2.4	0.0042	urine albumin amount (VT:0002871)	urine albumin excretion rate (CMO:0000757)	7	104603555	135012528	Rat
1358891	Bp265	Blood pressure QTL 265	2.21		arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	7	83591953	134666232	Rat

Hoxc13

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	7	134,064,551 - 134,064,780 (+)	MAPPER	mRatBN7.2
Rnor_6.0	7	144,537,718 - 144,537,946	NCBI	Rnor6.0
Rnor_5.0	7	142,329,075 - 142,329,303	UniSTS	Rnor5.0
Celera	7	130,490,793 - 130,491,021	UniSTS
Cytogenetic Map	7	q36	UniSTS

Hoxc13

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	7	134,058,981 - 134,059,061 (+)	MAPPER	mRatBN7.2
Rnor_6.0	7	144,532,156 - 144,532,235	NCBI	Rnor6.0
Rnor_5.0	7	142,323,513 - 142,323,592	UniSTS	Rnor5.0
Cytogenetic Map	7	q36	UniSTS

Click on a value in the shaded box below the category label to view a detailed expression data table for that system.

appendage	ectoderm	endocrine system	endoderm	integumental system	mesenchyme	mesoderm	nervous system	renal system	reproductive system	respiratory system
2	18	2	1	6	5	2	11	2	19	1


RefSeq Transcripts	XM_017603353	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_235695	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	JAXUCZ010000007	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

Ensembl Acc Id:

ENSRNOT00000033300 ⟹ ENSRNOP00000034124

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2 Ensembl	7	134,058,640 - 134,064,800 (+)	Ensembl
Rnor_6.0 Ensembl	7	144,531,814 - 144,537,966 (+)	Ensembl

RefSeq Acc Id:

XM_235695 ⟹ XP_235695

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
GRCr8	7	135,937,126 - 135,943,962 (+)	NCBI
mRatBN7.2	7	134,058,640 - 134,065,479 (+)	NCBI
Rnor_6.0	7	144,531,814 - 144,538,298 (+)	NCBI
Rnor_5.0	7	142,323,171 - 142,329,323 (+)	NCBI
RGSC_v3.4	7	141,685,004 - 141,691,159 (+)	RGD

Sequence:

show sequence

ATGACGACTTCGCTGCTCCTGCACCCGCGCTGGCCGGAGAGCCTTATGTACGTCTATGAGGACAGCGCGGCGGAGAGCGGCAGCGGCGGCGGCGGGGGAGGCGGCGGCGCGGGCGGCGCGGGGGGCGG
CTGTAGCGGCGCGAGCCCCGGCAAAGCCCCGAGCATGGACGGTCTGGGCGGCAGCTGCCCTGCCAGCCACTGCCGCGACCTGCTCCCGCACCCCGTGTTGGCCCGCCCGCCGGCTCCTCTGGGTGCCC
CTCAGGGCGCCGTCTACACGGACATCCCAGCCCCGGAGGCGGCGCGCCAATGCGCCCCACCGCCGGCGCCCCCCACCTCGTCCAGCGCCACCCTGGGCTACGGTTACCCATTTGGGGGCAGCTACTAC
GGCTGCCGCCTGTCGCACAACGTGAACCTGCAGCAGAAGCCTTGCTCCTACCATCCGGGAGACAAGTACCCAGAGCCGTCGGGCGCCCTGCCTGGTGACGACCTGTCCTCTAGGGCTAAGGAGTTCGC
CTTCTACCCCAGCTTCGCCAGCTCCTACCAGGCAATGCCCGGCTACCTGGACGTGTCGGTGGTGCCCGGGATCAGCGGGCACCCGGAGCCGCGTCACGACGCGCTCATCCCTGTTGAAGGCTACCAGC
ACTGGGCTCTTTCCAATGGCTGGGACAGTCAGGTGTACTGCTCCAAGGAGCAGTCGCAGTCCGCCCACCTCTGGAAGTCTCCCTTCCCAGACGTGGTTCCTCTACAGCCTGAAGTGAGCAGCTACCGG
CGCGGGCGCAAGAAGCGCGTGCCCTACACCAAGGTGCAGCTGAAGGAGCTAGAGAAGGAGTACGCAGCCAGCAAATTCATCACCAAAGAGAAGCGCCGGCGCATCTCAGCTACCACGAACCTCTCGGA
GCGCCAGGTCACCATCTGGTTCCAGAACCGGCGTGTGAAAGAGAAGAAGGTGGTCAGCAAATCGAAAGCGCCTCATCTCCACTCCACCTGACCTTCCTTTCGCCTGCCCTCCTGCCCCGACTATTTAT
GTCAGTGCTTTGTACCATAACAGAATTCACCCGAAGGACGCTGCACCGGCGCAGACCACTATTTAATCCTACCGAGAAAGAGGAACAGCTCTGCCTTACCCTAGTTCCATCCCACCCCTAATCTCACC
GCCCACCCCGCGCCAGTCGGCACCCACTCAGCACCCGCAGCTGTAGAGGTGGGTTCGAATGGGGTGCGAGAGGAAGACTGTCTCTAACCCCCCTGGCCTTGGTGGCTTGTCCCACTAGAAAGCCAAGT
GGCCAGGATAGCCCAGTAATTCCTACCAAAGCAGGACTG

hide sequence


Protein RefSeqs	XP_235695	(Get FASTA)	NCBI Sequence Viewer
Ensembl Protein	ENSRNOP00000034124
	ENSRNOP00000034124.4

RefSeq Acc Id:

XP_235695 ⟸ XM_235695

- UniProtKB:

D3ZKV8 (UniProtKB/TrEMBL)

- Sequence:

show sequence

MTTSLLLHPRWPESLMYVYEDSAAESGSGGGGGGGGAGGAGGGCSGASPGKAPSMDGLGGSCPASHCRDLLPHPVLARPPAPLGAPQGAVYTDIPAPEAARQCAPPPAPPTSSSATLGYGYPFGGSYY
GCRLSHNVNLQQKPCSYHPGDKYPEPSGALPGDDLSSRAKEFAFYPSFASSYQAMPGYLDVSVVPGISGHPEPRHDALIPVEGYQHWALSNGWDSQVYCSKEQSQSAHLWKSPFPDVVPLQPEVSSYR
RGRKKRVPYTKVQLKELEKEYAASKFITKEKRRRISATTNLSERQVTIWFQNRRVKEKKVVSKSKAPHLHST

hide sequence

Ensembl Acc Id:

ENSRNOP00000034124 ⟸ ENSRNOT00000033300

Protein Domains

Homeobox

Name	Modeler	Protein Id	AA Range	Protein Structure
AF-D3ZKV8-F1-model_v2	AlphaFold	D3ZKV8	1-328	view protein structure

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

RGD ID:

13695712

Promoter ID:

EPDNEW_R6234

Type:

multiple initiation site

Name:

Hoxc13_1

Description:

homeobox C13

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	7	144,531,887 - 144,531,947	EPDNEW

Database	Acc Id	Source(s)
BioCyc Gene	G2FUF-31922	BioCyc
Ensembl Genes	ENSRNOG00000028679	Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript	ENSRNOT00000033300	ENTREZGENE
	ENSRNOT00000033300.5	UniProtKB/TrEMBL
Gene3D-CATH	Homeodomain-like	UniProtKB/TrEMBL
InterPro	AP_axis_regulatory_Homeobox	UniProtKB/TrEMBL
	Homeobox	UniProtKB/TrEMBL
	Homeobox_CS	UniProtKB/TrEMBL
	Homeodomain-like	UniProtKB/TrEMBL
	HoxA13_N	UniProtKB/TrEMBL
KEGG Report	rno:315337	UniProtKB/TrEMBL
NCBI Gene	315337	ENTREZGENE
PANTHER	HOMEOBOX PROTEIN HOX-C13	UniProtKB/TrEMBL
	SEGMENTATION PROTEIN FUSHI TARAZU-LIKE PROTEIN	UniProtKB/TrEMBL
Pfam	Homeobox	UniProtKB/TrEMBL
	HoxA13_N	UniProtKB/TrEMBL
PhenoGen	Hoxc13	PhenoGen
PROSITE	HOMEOBOX_1	UniProtKB/TrEMBL
	HOMEOBOX_2	UniProtKB/TrEMBL
RatGTEx	ENSRNOG00000028679	RatGTEx
SMART	HOX	UniProtKB/TrEMBL
Superfamily-SCOP	Homeodomain_like	UniProtKB/TrEMBL
UniProt	D3ZKV8	ENTREZGENE, UniProtKB/TrEMBL

Nomenclature History

Date	Current Symbol	Current Name	Previous Symbol	Previous Name	Description	Reference	Status
2008-03-07	Hoxc13	homeobox C13	RGD1563984_predicted	similar to homeodomain protein (predicted)	Nomenclature updated to reflect human and mouse nomenclature	1299863	APPROVED
2006-03-07	RGD1563984_predicted	similar to homeodomain protein (predicted)	LOC315337	similar to homeodomain protein	Symbol and Name status set to approved	1299863	APPROVED
2006-02-09	LOC315337	similar to homeodomain protein			Symbol and Name status set to provisional	70820	PROVISIONAL

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


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


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