Hoxc9 (homeobox C9) - Rat Genome Database

Name: Hoxc9
Creator: Rat Genome Database
License: Creative Commons CC BY 4.0
Keywords: Rat Gene RGD Genome

Gene: Hoxc9 (homeobox C9) Rattus norvegicus

Analyze

Symbol:

Hoxc9

Name:

homeobox C9

RGD ID:

1595784

Description:

Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific and RNA polymerase II transcription regulatory region sequence-specific DNA binding activity. Predicted to be involved in regulation of transcription by RNA polymerase II. Predicted to act upstream of or within anterior/posterior pattern specification and embryonic skeletal system morphogenesis. Predicted to be located in aggresome and nucleoplasm. Predicted to be part of transcription repressor complex. Predicted to be active in nucleus. Orthologous to human HOXC9 (homeobox C9); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; acrylamide; atrazine.

Type:

protein-coding

RefSeq Status:

VALIDATED

Previously known as:

homeo box C9; homeobox protein Hox-C9; Hoxc8; LOC300264

RGD Orthologs

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):	HOXC9 (homeobox C9)	HGNC	Ensembl, HomoloGene, NCBI, OMA, OrthoDB, OrthoMCL, PhylomeDB, Treefam
Mus musculus (house mouse):	Hoxc9 (homeobox C9)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chinchilla lanigera (long-tailed chinchilla):	Hoxc9 (homeobox C9)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Pan paniscus (bonobo/pygmy chimpanzee):	HOXC9 (homeobox C9)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Canis lupus familiaris (dog):	HOXC9 (homeobox C9)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Ictidomys tridecemlineatus (thirteen-lined ground squirrel):	Hoxc9 (homeobox C9)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Sus scrofa (pig):	HOXC9 (homeobox C9)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chlorocebus sabaeus (green monkey):	HOXC9 (homeobox C9)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Heterocephalus glaber (naked mole-rat):	Hoxc9 (homeobox C9)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Other homologs ²
Homo sapiens (human):	HOXD8 (homeobox D8)	HGNC	Panther
Alliance orthologs ³
Homo sapiens (human):	HOXC9 (homeobox C9)	Alliance	DIOPT (Ensembl Compara\|HGNC\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PhylomeDB\|SonicParanoid)
Mus musculus (house mouse):	Hoxc9 (homeobox C9)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PhylomeDB\|SonicParanoid)
Danio rerio (zebrafish):	hoxc9a (homeobox C9a)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PhylomeDB\|SonicParanoid)
Xenopus tropicalis (tropical clawed frog):	hoxc9	Alliance	DIOPT (Ensembl Compara\|OMA\|OrthoFinder)

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
GRCr8	7	135,997,292 - 135,999,969 (+)	NCBI		GRCr8
mRatBN7.2	7	134,118,817 - 134,121,497 (+)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	7	134,118,817 - 134,121,492 (+)	Ensembl		mRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx	7	135,874,221 - 135,876,886 (+)	NCBI	Rnor_SHR	UTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0	7	138,103,596 - 138,106,261 (+)	NCBI	Rnor_SHRSP	UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0	7	138,089,529 - 138,092,226 (+)	NCBI	Rnor_WKY	UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0	7	144,592,462 - 144,598,807 (+)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	7	144,595,960 - 144,598,632 (+)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	7	142,383,988 - 142,390,164 (+)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	7	141,745,173 - 141,775,242 (+)	NCBI	RGSC3.4	RGSC_v3.4	rn4	RGSC3.4
Celera	7	130,544,848 - 130,547,525 (+)	NCBI		Celera
Cytogenetic Map	7	q36	NCBI

JBrowse:

View Region in Genome Browser (JBrowse)

Model

Annotation Click to see Annotation Detail View

Disease Annotations Click to see Annotation Detail View

genetic disease (ISO)

Neurodevelopmental Disorders (ISO)

Gene-Chemical Interaction Annotations Click to see Annotation Detail View

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

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

acrylamide (EXP)

aflatoxin B1 (ISO)

all-trans-retinoic acid (ISO)

antirheumatic drug (ISO)

aristolochic acid A (ISO)

arsenite(3-) (ISO)

arsenous acid (ISO)

atrazine (EXP)

benzo[a]pyrene (ISO)

bis(2-chloroethyl) sulfide (ISO)

bisphenol A (ISO)

bisphenol F (ISO)

cadmium atom (ISO)

cadmium dichloride (ISO)

cisplatin (ISO)

copper(II) sulfate (ISO)

dexamethasone (ISO)

diarsenic trioxide (ISO)

FR900359 (ISO)

fructose (EXP)

fulvestrant (ISO)

genistein (ISO)

indometacin (ISO)

nickel atom (ISO)

nickel sulfate (ISO)

oxaliplatin (EXP)

ozone (EXP)

paracetamol (EXP)

potassium chromate (ISO)

temozolomide (ISO)

thapsigargin (ISO)

titanium dioxide (ISO)

topotecan (EXP)

trichloroethene (EXP)

triclosan (ISO)

tunicamycin (ISO)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

anterior/posterior pattern specification (ISO)

DNA-templated transcription (IEA)

embryonic skeletal system development (ISO)

embryonic skeletal system morphogenesis (ISO)

proximal/distal pattern formation (IEA)

regulation of transcription by RNA polymerase II (IBA)

Cellular Component

aggresome (IEA,ISO)

nucleoplasm (IEA,ISO)

nucleus (IBA)

transcription repressor complex (ISO)

Molecular Function

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

protein binding (ISO)

RNA polymerase II cis-regulatory region sequence-specific DNA binding (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.	Chromosomal assignment of seven rat homeobox genes to rat chromosomes 3, 4, 7, and 10.	Chung SY, etal., Mamm Genome 1993 Sep;4(9):537-40.
2.	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.
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

Additional References at PubMed

PMID:2907739	PMID:7547473	PMID:7702549	PMID:8889548	PMID:11870622	PMID:17626057

Genomics

Comparative Map Data

Hoxc9
(Rattus norvegicus - Norway rat)

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCr8	7	135,997,292 - 135,999,969 (+)	NCBI		GRCr8
mRatBN7.2	7	134,118,817 - 134,121,497 (+)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	7	134,118,817 - 134,121,492 (+)	Ensembl		mRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx	7	135,874,221 - 135,876,886 (+)	NCBI	Rnor_SHR	UTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0	7	138,103,596 - 138,106,261 (+)	NCBI	Rnor_SHRSP	UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0	7	138,089,529 - 138,092,226 (+)	NCBI	Rnor_WKY	UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0	7	144,592,462 - 144,598,807 (+)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	7	144,595,960 - 144,598,632 (+)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	7	142,383,988 - 142,390,164 (+)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	7	141,745,173 - 141,775,242 (+)	NCBI	RGSC3.4	RGSC_v3.4	rn4	RGSC3.4
Celera	7	130,544,848 - 130,547,525 (+)	NCBI		Celera
Cytogenetic Map	7	q36	NCBI

HOXC9
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38	12	54,000,161 - 54,003,337 (+)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh38.p14 Ensembl	12	53,994,895 - 54,003,337 (+)	Ensembl	GRCh38		hg38	GRCh38
GRCh37	12	54,393,945 - 54,397,121 (+)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	12	52,680,144 - 52,683,388 (+)	NCBI	NCBI36	Build 36	hg18	NCBI36
Build 34	12	52,680,143 - 52,683,385	NCBI
Celera	12	54,043,494 - 54,046,738 (+)	NCBI		Celera
Cytogenetic Map	12	q13.13	NCBI
HuRef	12	51,431,589 - 51,434,833 (+)	NCBI		HuRef
CHM1_1	12	54,360,582 - 54,363,824 (+)	NCBI		CHM1_1
T2T-CHM13v2.0	12	53,965,683 - 53,968,859 (+)	NCBI		T2T-CHM13v2.0

Hoxc9
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	15	102,885,467 - 102,893,324 (+)	NCBI	GRCm39	GRCm39	mm39
GRCm39 Ensembl	15	102,884,874 - 102,893,531 (+)	Ensembl		GRCm39 Ensembl
GRCm38	15	102,977,032 - 102,984,444 (+)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	15	102,976,439 - 102,985,099 (+)	Ensembl	GRCm38		mm10	GRCm38
MGSCv37	15	102,807,463 - 102,814,875 (+)	NCBI	GRCm37	MGSCv37	mm9	NCBIm37
MGSCv36	15	102,805,066 - 102,812,478 (+)	NCBI		MGSCv36	mm8
Celera	15	105,137,957 - 105,145,366 (+)	NCBI		Celera
Cytogenetic Map	15	F3	NCBI
cM Map	15	58.04	NCBI

Hoxc9
(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	1,258,364 - 1,261,510 (+)	Ensembl	ChiLan1.0
ChiLan1.0	NW_004955458	1,258,364 - 1,261,510 (+)	NCBI	ChiLan1.0	ChiLan1.0

HOXC9
(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	40,182,580 - 40,191,726 (-)	NCBI		NHGRI_mPanPan1-v2
NHGRI_mPanPan1	12	40,179,234 - 40,184,613 (-)	NCBI		NHGRI_mPanPan1
Mhudiblu_PPA_v0	12	34,751,922 - 34,755,157 (-)	NCBI	Mhudiblu_PPA_v0	Mhudiblu_PPA_v0	panPan3
PanPan1.1	12	35,540,234 - 35,543,486 (-)	NCBI	panpan1.1	PanPan1.1	panPan2
PanPan1.1 Ensembl	12	35,540,234 - 35,543,486 (-)	Ensembl	panpan1.1		panPan2

HOXC9
(Canis lupus familiaris - dog)

Dog Assembly	Chr	Position (strand)	Source	Genome Browsers
Dog Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Dog10K_Boxer_Tasha	27	44,986,842 - 44,990,561 (+)	NCBI		Dog10K_Boxer_Tasha
ROS_Cfam_1.0	27	1,262,717 - 1,266,438 (-)	NCBI		ROS_Cfam_1.0
UMICH_Zoey_3.1	27	1,280,424 - 1,284,140 (-)	NCBI		UMICH_Zoey_3.1
UNSW_CanFamBas_1.0	27	1,261,960 - 1,265,657 (-)	NCBI		UNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0	27	45,390,457 - 45,394,183 (+)	NCBI		UU_Cfam_GSD_1.0

Hoxc9
(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	61,939,375 - 61,942,710 (-)	NCBI		HiC_Itri_2
SpeTri2.0 Ensembl	NW_004936512	11,217,547 - 11,225,455 (+)	Ensembl	SpeTri2.0	SpeTri2.0 Ensembl
SpeTri2.0	NW_004936512	11,222,120 - 11,225,455 (+)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

HOXC9
(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	19,212,905 - 19,215,984 (+)	Ensembl	Sscrofa11.1		susScr11	Sscrofa11.1
Sscrofa11.1	5	19,212,490 - 19,215,859 (+)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1
Sscrofa10.2	5	19,637,238 - 19,644,861 (-)	NCBI	Sscrofa10.2	Sscrofa10.2	susScr3

HOXC9
(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	50,110,729 - 50,113,986 (+)	NCBI	ChlSab1.1	ChlSab1.1	chlSab2
ChlSab1.1 Ensembl	11	50,110,753 - 50,113,975 (+)	Ensembl	ChlSab1.1	ChlSab1.1 Ensembl	chlSab2
Vero_WHO_p1.0	NW_023666037	195,928,198 - 195,931,419 (-)	NCBI	Vero_WHO_p1.0	Vero_WHO_p1.0

Hoxc9
(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	2,054,386 - 2,058,539 (+)	Ensembl	HetGla_female_1.0	HetGla_female_1.0 Ensembl	hetGla2
HetGla 1.0	NW_004624904	2,054,768 - 2,058,556 (+)	NCBI	HetGla_female_1.0	HetGla 1.0	hetGla2

Variants

Variants in Hoxc9
7 total Variants

miRNA Target Status

Predicted Target Of

	Summary Value
Count of predictions:	62
Count of miRNA genes:	55
Interacting mature miRNAs:	56
Transcripts:	ENSRNOT00000021909
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.

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
1300179	Kidm5	Kidney mass QTL 5	3.51		kidney mass (VT:0002707)	left kidney wet weight (CMO:0000083)	7	43747012	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
1358891	Bp265	Blood pressure QTL 265	2.21		arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	7	83591953	134666232	Rat
1358914	Bp266	Blood pressure QTL 266			arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	7	83591953	134666232	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
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
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
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
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
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
1354582	Stl11	Serum triglyceride level QTL 11	3.42		blood triglyceride amount (VT:0002644)	serum triglyceride level (CMO:0000360)	7	119513385	135012528	Rat

Markers in Region

Hoxc8

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	7	134,129,956 - 134,130,058 (+)	MAPPER	mRatBN7.2
Rnor_6.0	7	144,607,093 - 144,607,194	NCBI	Rnor6.0
Rnor_5.0	7	142,398,450 - 142,398,551	UniSTS	Rnor5.0
RGSC_v3.4	7	141,756,303 - 141,756,404	UniSTS	RGSC3.4
Celera	7	130,555,856 - 130,555,957	UniSTS
Cytogenetic Map	7	q35	UniSTS
Cytogenetic Map	7	q36	UniSTS

Hoxc9

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	7	134,121,169 - 134,121,357 (+)	MAPPER	mRatBN7.2
Rnor_6.0	7	144,598,310 - 144,598,497	NCBI	Rnor6.0
Rnor_5.0	7	142,389,667 - 142,389,854	UniSTS	Rnor5.0
RGSC_v3.4	7	141,747,523 - 141,747,710	UniSTS	RGSC3.4
Celera	7	130,547,198 - 130,547,385	UniSTS
Cytogenetic Map	7	q35	UniSTS
Cytogenetic Map	7	q36	UniSTS

PMC15172P2

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	7	134,121,115 - 134,121,492 (+)	MAPPER	mRatBN7.2
Rnor_6.0	7	144,598,256 - 144,598,632	NCBI	Rnor6.0
Rnor_5.0	7	142,389,613 - 142,389,989	UniSTS	Rnor5.0
RGSC_v3.4	7	141,747,469 - 141,747,845	UniSTS	RGSC3.4
Celera	7	130,547,144 - 130,547,520	UniSTS
Cytogenetic Map	7	q35	UniSTS
Cytogenetic Map	7	q36	UniSTS

MARC_41665-41666:1086710236:1

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	7	134,128,189 - 134,129,758 (+)	MAPPER	mRatBN7.2
Rnor_6.0	7	144,605,325 - 144,606,894	NCBI	Rnor6.0
Rnor_5.0	7	142,396,682 - 142,398,251	UniSTS	Rnor5.0
RGSC_v3.4	7	141,754,536 - 141,756,104	UniSTS	RGSC3.4
Celera	7	130,554,088 - 130,555,657	UniSTS
Cytogenetic Map	7	q35	UniSTS
Cytogenetic Map	7	q36	UniSTS

MARC_46193-46194:1108499233:1

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	7	134,136,958 - 134,137,573 (+)	MAPPER	mRatBN7.2
Rnor_6.0	7	144,614,095 - 144,614,709	NCBI	Rnor6.0
Rnor_5.0	7	142,405,452 - 142,406,066	UniSTS	Rnor5.0
RGSC_v3.4	7	141,763,306 - 141,763,920	UniSTS	RGSC3.4
Celera	7	130,562,858 - 130,563,472	UniSTS
Cytogenetic Map	7	q35	UniSTS
Cytogenetic Map	7	q36	UniSTS

Hoxc9

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	7	134,118,954 - 134,119,058 (+)	MAPPER	mRatBN7.2
Rnor_6.0	7	144,592,790 - 144,592,893	NCBI	Rnor6.0
Rnor_6.0	7	144,596,098 - 144,596,201	NCBI	Rnor6.0
Rnor_5.0	7	142,387,455 - 142,387,558	UniSTS	Rnor5.0
Rnor_5.0	7	142,384,147 - 142,384,250	UniSTS	Rnor5.0
Celera	7	130,544,986 - 130,545,089	UniSTS
Cytogenetic Map	7	q35	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	endocrine system	exocrine system	hemolymphoid system	hepatobiliary system	integumental system	musculoskeletal system	renal system	reproductive system	respiratory system	appendage
High
Medium							1	17	19
Low	1	4				8	10	18	21		8
Below cutoff	2	8	1	8	1				1	2

View RNA-SEQ Expression Data

Sequence

Nucleotide Sequences


RefSeq Transcripts	NM_001100907	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_006242434	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	AC116663	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	BQ205031	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	JAXUCZ010000007	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

RefSeq Acc Id:

ENSRNOT00000021909 ⟹ ENSRNOP00000021910

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2 Ensembl	7	134,118,817 - 134,121,492 (+)	Ensembl
Rnor_6.0 Ensembl	7	144,595,960 - 144,598,632 (+)	Ensembl

RefSeq Acc Id:

NM_001100907 ⟹ NP_001094377

RefSeq Status:

VALIDATED

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
GRCr8	7	135,997,292 - 135,999,969 (+)	NCBI
mRatBN7.2	7	134,118,817 - 134,121,497 (+)	NCBI
Rnor_6.0	7	144,595,960 - 144,598,637 (+)	NCBI
Rnor_5.0	7	142,383,988 - 142,390,164 (+)	NCBI
Celera	7	130,544,848 - 130,547,525 (+)	NCBI

Sequence:

show sequence

ATGTCGGCGACGGGGCCCATCAGTAACTATTACGTGGACTCGCTCATCTCTCACGACAATGAAG
ACCTCCTAGCGTCCAGGTTTCCGGCCACCGGGGCTCACCCTGCCGCCGCCAGACCCAGCGGCTT
GGTGCCGGACTGTAGCGATTTTCCGTCCTGTAGCTTCGCGCCCAAGCCGGCTGTATTCAGCACG
TCGTGGGCGCCCGTGCCCTCGCAGTCGTCCGTGGTCTATCACCCTTACGGCCCCCAGCCCCACC
TCGGCGCCGACACGCGCTACATGCGGACTTGGCTCGAGCCGCTGTCCGGCGCCGTCTCCTTCCC
CAGCTTCCCAGCCGGGGGCCGTCACTACGCCCTCAAGCCCGACGCCTACCCCGGGCGCCGCGCC
GACTGCGGCCCGGGCGACGGCCGCAGCTACCCGGACTACATGTACGGCTCTCCCGGGGAACTGC
GCGACCGCGCCCCGCAGACGCTGCCCTCGCCCGAGGCGGACGCGCTGGCCGGCAGCAAGCACAA
AGAGGAGAAGGCCGACCTGGACCCTAGCAACCCCGTGGCCAACTGGATCCATGCCCGTTCCACA
AGGAAGAAGCGCTGCCCCTACACCAAGTACCAGACGCTGGAACTGGAGAAGGAGTTTCTCTTCA
ATATGTATTTAACTAGGGACCGTCGGTACGAGGTGGCCCGTGTTCTCAATCTCACTGAGCGGCA
GGTCAAAATCTGGTTTCAGAACCGGAGGATGAAAATGAAAAAGATGAATAAAGAAAAAACCGAC
AAAGAACAATCCTAAACCCTGCCCCAGCCTGCTGCCTCGGCACAGCCAAGGGAAACACAAAAAC
CCCACCAAAAAATGCCCCAACTCAGGCGGGAGAAAGCACGAAAAGAAAAGGAAAGAACAAGATA
GAGAAAAGCCCAACGTCTTAAAAA

hide sequence

Protein Sequences


Protein RefSeqs	NP_001094377	(Get FASTA)	NCBI Sequence Viewer
Ensembl Protein	ENSRNOP00000021910
	ENSRNOP00000021910.4

RefSeq Acc Id:

NP_001094377 ⟸ NM_001100907

- UniProtKB:

D4A0V9 (UniProtKB/TrEMBL), A6KCY8 (UniProtKB/TrEMBL)

- Sequence:

show sequence

MSATGPISNYYVDSLISHDNEDLLASRFPATGAHPAAARPSGLVPDCSDFPSCSFAPKPAVFST
SWAPVPSQSSVVYHPYGPQPHLGADTRYMRTWLEPLSGAVSFPSFPAGGRHYALKPDAYPGRRA
DCGPGDGRSYPDYMYGSPGELRDRAPQTLPSPEADALAGSKHKEEKADLDPSNPVANWIHARST
RKKRCPYTKYQTLELEKEFLFNMYLTRDRRYEVARVLNLTERQVKIWFQNRRMKMKKMNKEKTD
KEQS

hide sequence

RefSeq Acc Id:

ENSRNOP00000021910 ⟸ ENSRNOT00000021909

Protein Domains

Homeobox

Protein Structures

Name	Modeler	Protein Id	AA Range	Protein Structure
AF-D4A0V9-F1-model_v2	AlphaFold	D4A0V9	1-260	view protein structure

Transcriptome

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

Promoters

RGD ID:

13695710

Promoter ID:

EPDNEW_R6235

Type:

single initiation site

Name:

Hoxc9_1

Description:

homeobox C9

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	144,595,932 - 144,595,992	EPDNEW

Additional Information

External Database Links

Database	Acc Id	Source(s)
AGR Gene	RGD:1595784	AgrOrtholog
BioCyc Gene	G2FUF-31913	BioCyc
Ensembl Genes	ENSRNOG00000016199	Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript	ENSRNOT00000021909	ENTREZGENE
	ENSRNOT00000021909.6	UniProtKB/TrEMBL
Gene3D-CATH	Homeodomain-like	UniProtKB/TrEMBL
InterPro	Homeobox-like	UniProtKB/TrEMBL
	Homeobox_CS	UniProtKB/TrEMBL
	Homeobox_dom	UniProtKB/TrEMBL
	Homeobox_Hox9	UniProtKB/TrEMBL
	Homeobox_metazoa	UniProtKB/TrEMBL
	Hox9_activation_N	UniProtKB/TrEMBL
KEGG Report	rno:368178	UniProtKB/TrEMBL
NCBI Gene	368178	ENTREZGENE
PANTHER	AGAP004664-PA	UniProtKB/TrEMBL
	HOMEOBOX PROTEIN HOX-C9	UniProtKB/TrEMBL
Pfam	Homeobox	UniProtKB/TrEMBL
	Hox9_act	UniProtKB/TrEMBL
PhenoGen	Hoxc9	PhenoGen
PIRSF	Homeobox_Hox9	UniProtKB/TrEMBL
PRINTS	HOMEOBOX	UniProtKB/TrEMBL
PROSITE	HOMEOBOX_1	UniProtKB/TrEMBL
	HOMEOBOX_2	UniProtKB/TrEMBL
RatGTEx	ENSRNOG00000016199	RatGTEx
SMART	HOX	UniProtKB/TrEMBL
Superfamily-SCOP	SSF46689	UniProtKB/TrEMBL
UniProt	A6KCY8	ENTREZGENE, UniProtKB/TrEMBL
	D4A0V9	ENTREZGENE, UniProtKB/TrEMBL

Nomenclature History

Date	Current Symbol	Current Name	Previous Symbol	Previous Name	Description	Reference	Status
2009-06-15	Hoxc9	homeobox C9	Hoxc9_predicted	homeo box C9 (predicted)	Data merged from RGD:1305802	1643240	APPROVED
2008-03-04	Hoxc9	homeobox C9	Hoxc8	homeo box C8	Nomenclature updated to reflect human and mouse nomenclature	1299863	APPROVED
2007-04-13		homeo box C8	Hoxc8	homeo box C8 (mapped)	Name updated	737654	APPROVED
2007-04-11	Hoxc8	homeo box C8 (mapped)	Hoxc8_mapped	homeo box C8 (mapped)	Data merged from RGD:2821	737654	APPROVED
2006-11-20	Hoxc8	homeo box C8 (mapped)			Symbol and Name status set to provisional	70820	PROVISIONAL
2005-11-17	Hoxc8_mapped	homeo box C8 (mapped)	Hoxc8	homeo box C8	Symbol and Name updated	1556543	APPROVED
2005-01-12	Hoxc9_predicted	homeo box C9 (predicted)			Symbol and Name status set to approved	70820	APPROVED
2002-06-10	Hoxc8	Homeobox gene C8			Symbol and Name status set to approved	70586	APPROVED

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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