Hoxc11 (homeobox C11) - Rat Genome Database

Name: Hoxc11
Creator: Rat Genome Database
License: Creative Commons CC BY 4.0
Keywords: Rat Gene RGD Genome

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Gene: Hoxc11 (homeobox C11) Ictidomys tridecemlineatus

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Symbol:

Hoxc11

Name:

homeobox C11

RGD ID:

12493520

Description:

ENCODES a protein that exhibits DNA binding (inferred); DNA-binding transcription activator activity, RNA polymerase II-specific (inferred); DNA-binding transcription factor activity, RNA polymerase II-specific (inferred); INVOLVED IN anterior/posterior pattern specification (ortholog); embryonic digit morphogenesis (ortholog); embryonic skeletal joint morphogenesis (ortholog); ASSOCIATED WITH Neurodevelopmental Disorders (ortholog); FOUND IN cytosol (inferred); nucleoplasm (inferred); nucleus (inferred)

Type:

protein-coding

RefSeq Status:

MODEL

Previously known as:

homeobox protein Hox-C11

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):	HOXC11 (homeobox C11)	NCBI	Ortholog
Mus musculus (house mouse):	Hoxc11 (homeobox C11)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Rattus norvegicus (Norway rat):	Hoxc11 (homeobox C11)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chinchilla lanigera (long-tailed chinchilla):	Hoxc11 (homeobox C11)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Pan paniscus (bonobo/pygmy chimpanzee):	HOXC11 (homeobox C11)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Canis lupus familiaris (dog):	HOXC11 (homeobox C11)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Sus scrofa (pig):	HOXC11 (homeobox C11)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chlorocebus sabaeus (green monkey):	LOC103238414 (uncharacterized LOC103238414)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Heterocephalus glaber (naked mole-rat):	Hoxc11 (homeobox C11)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline

Latest Assembly:

SpeTri2.0 - Squirrel SpeTri2.0 Assembly

Position:

Squirrel Assembly	Chr	Position (strand)	Source	Genome Browsers
Squirrel Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
HiC_Itri_2	NW_024404945	61,967,514 - 61,970,059 (-)	NCBI		HiC_Itri_2
SpeTri2.0 Ensembl	NW_004936512	11,194,876 - 11,197,316 (+)	Ensembl	SpeTri2.0	SpeTri2.0 Ensembl
SpeTri2.0	NW_004936512	11,194,876 - 11,197,316 (+)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

JBrowse:

View Region in Genome Browser (JBrowse)

Model

Annotation Click to see Annotation Detail View

Disease Annotations Click to see Annotation Detail View

Neurodevelopmental Disorders (ISO)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

anterior/posterior pattern specification (IEA,ISO)

embryonic digit morphogenesis (IEA,ISO)

embryonic skeletal joint morphogenesis (IEA,ISO)

metanephros development (IEA,ISO)

organ induction (IEA,ISO)

positive regulation of transcription by RNA polymerase II (IEA)

proximal/distal pattern formation (IEA,ISO)

regulation of DNA-templated transcription (IEA)

regulation of transcription by RNA polymerase II (IEA)

skeletal system development (IEA,ISO)

Cellular Component

cytosol (IEA)

nucleoplasm (IEA)

nucleus (IEA)

Molecular Function

DNA binding (IEA)

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

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

protein binding (ISO)

RNA polymerase II cis-regulatory region sequence-specific DNA binding (IEA)

sequence-specific double-stranded DNA binding (IEA)

References

Additional References at PubMed

PMID:22301074	PMID:30032202

Genomics

Comparative Map Data

Hoxc11
(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	61,967,514 - 61,970,059 (-)	NCBI		HiC_Itri_2
SpeTri2.0 Ensembl	NW_004936512	11,194,876 - 11,197,316 (+)	Ensembl	SpeTri2.0	SpeTri2.0 Ensembl
SpeTri2.0	NW_004936512	11,194,876 - 11,197,316 (+)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

HOXC11
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38	12	53,973,126 - 53,977,643 (+)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh38.p14 Ensembl	12	53,973,126 - 53,977,643 (+)	Ensembl	GRCh38		hg38	GRCh38
GRCh37	12	54,366,910 - 54,371,427 (+)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	12	52,653,177 - 52,656,470 (+)	NCBI	NCBI36	Build 36	hg18	NCBI36
Build 34	12	52,653,195 - 52,656,468	NCBI
Celera	12	54,016,511 - 54,019,822 (+)	NCBI		Celera
Cytogenetic Map	12	q13.13	NCBI
HuRef	12	51,404,138 - 51,407,449 (+)	NCBI		HuRef
CHM1_1	12	54,333,599 - 54,336,910 (+)	NCBI		CHM1_1
T2T-CHM13v2.0	12	53,938,618 - 53,943,153 (+)	NCBI		T2T-CHM13v2.0

Hoxc11
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	15	102,862,961 - 102,865,136 (+)	NCBI	GRCm39	GRCm39	mm39
GRCm39 Ensembl	15	102,862,862 - 102,866,143 (+)	Ensembl		GRCm39 Ensembl
GRCm38	15	102,954,526 - 102,956,701 (+)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	15	102,954,427 - 102,957,708 (+)	Ensembl	GRCm38		mm10	GRCm38
MGSCv37	15	102,784,957 - 102,787,132 (+)	NCBI	GRCm37	MGSCv37	mm9	NCBIm37
MGSCv36	15	102,782,560 - 102,784,735 (+)	NCBI		MGSCv36	mm8
Celera	15	105,115,456 - 105,117,632 (+)	NCBI		Celera
Cytogenetic Map	15	F3	NCBI
cM Map	15	58.02	NCBI

Hoxc11
(Rattus norvegicus - Norway rat)

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCr8	7	135,969,707 - 135,973,222 (+)	NCBI		GRCr8
mRatBN7.2	7	134,091,224 - 134,094,738 (+)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	7	134,091,552 - 134,094,738 (+)	Ensembl		mRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx	7	135,846,891 - 135,850,122 (+)	NCBI	Rnor_SHR	UTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0	7	138,076,265 - 138,079,496 (+)	NCBI	Rnor_SHRSP	UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0	7	138,062,254 - 138,065,485 (+)	NCBI	Rnor_WKY	UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0	7	144,565,392 - 144,568,580 (+)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	7	144,565,392 - 144,567,580 (+)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	7	142,356,703 - 142,358,942 (+)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
Celera	7	130,517,972 - 130,520,959 (+)	NCBI		Celera
Cytogenetic Map	7	q36	NCBI

Hoxc11
(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	1,231,445 - 1,234,798 (+)	Ensembl	ChiLan1.0
ChiLan1.0	NW_004955458	1,231,625 - 1,234,785 (+)	NCBI	ChiLan1.0	ChiLan1.0

HOXC11
(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	40,209,471 - 40,213,236 (-)	NCBI		NHGRI_mPanPan1-v2
NHGRI_mPanPan1	12	40,201,196 - 40,209,548 (-)	NCBI		NHGRI_mPanPan1
Mhudiblu_PPA_v0	12	34,777,790 - 34,782,104 (-)	NCBI	Mhudiblu_PPA_v0	Mhudiblu_PPA_v0	panPan3
PanPan1.1	12	35,567,093 - 35,570,396 (-)	NCBI	panpan1.1	PanPan1.1	panPan2
PanPan1.1 Ensembl	12	35,567,093 - 35,570,396 (-)	Ensembl	panpan1.1		panPan2

HOXC11
(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	1,287,326 - 1,289,577 (-)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1
CanFam3.1 Ensembl	27	1,287,380 - 1,289,372 (-)	Ensembl	CanFam3.1		canFam3	CanFam3.1
Dog10K_Boxer_Tasha	27	44,960,239 - 44,962,245 (+)	NCBI		Dog10K_Boxer_Tasha
ROS_Cfam_1.0	27	1,291,036 - 1,293,043 (-)	NCBI		ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl	27	1,291,044 - 1,293,036 (-)	Ensembl		ROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1	27	1,308,728 - 1,310,736 (-)	NCBI		UMICH_Zoey_3.1
UNSW_CanFamBas_1.0	27	1,290,305 - 1,292,309 (-)	NCBI		UNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0	27	45,363,845 - 45,365,853 (+)	NCBI		UU_Cfam_GSD_1.0

HOXC11
(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	19,178,619 - 19,189,013 (+)	Ensembl	Sscrofa11.1		susScr11	Sscrofa11.1
Sscrofa11.1	5	19,181,580 - 19,189,031 (+)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1
Sscrofa10.2	5	19,685,024 - 19,687,605 (+)	NCBI	Sscrofa10.2	Sscrofa10.2	susScr3

LOC103238414
(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	50,076,648 - 50,087,084 (+)	NCBI	ChlSab1.1	ChlSab1.1	chlSab2
ChlSab1.1 Ensembl	11	50,083,893 - 50,086,060 (+)	Ensembl	ChlSab1.1	ChlSab1.1 Ensembl	chlSab2
Vero_WHO_p1.0	NW_023666037	195,964,311 - 195,965,531 (-)	NCBI	Vero_WHO_p1.0	Vero_WHO_p1.0

Hoxc11
(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	2,027,993 - 2,030,148 (+)	Ensembl	HetGla_female_1.0	HetGla_female_1.0 Ensembl	hetGla2
HetGla 1.0	NW_004624904	2,027,792 - 2,030,148 (+)	NCBI	HetGla_female_1.0	HetGla 1.0	hetGla2

Expression

RNA-SEQ Expression

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

Sequence

Nucleotide Sequences


RefSeq Transcripts	XM_005325063	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	JAESOR010000004	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

Ensembl Acc Id:

ENSSTOT00000027675 ⟹ ENSSTOP00000019763

Type:

CODING

Position:

Squirrel Assembly	Chr	Position (strand)	Source
SpeTri2.0 Ensembl	NW_004936512	11,194,876 - 11,197,316 (+)	Ensembl

RefSeq Acc Id:

XM_005325063 ⟹ XP_005325120

Type:

CODING

Position:

Squirrel Assembly	Chr	Position (strand)	Source
HiC_Itri_2	NW_024404945	61,967,514 - 61,970,059 (-)	NCBI
SpeTri2.0	NW_004936512	11,194,876 - 11,197,316 (+)	NCBI

Sequence:

show sequence

GAGAGAGACTAAGACGGATAACGCGTCATCTCGCCTTCCCAAAATTTCCCCCCTCACTAGACCG
GGTCCAAAACCTCCATCCGGAGCCGGCAGGAGAGGAGAACGATGTTTAACTCGGTCAACCTGGG
CAACTTCTGCTCGCCGTCGCGCAAAGAGAGGGGCGCTGACTTCGGCGAGCGAGGGAGCTGCGCC
TCCAACCTCTATCTACCCAGTTGCACTTACTACGTGCCCGAGTTCTCCACGGTCTCCTCCTTCC
TGCCCCAAGCCCCCTCTCGTCAGATCTCCTATCCCTACTCGGCCCAAGTGCCCCCGGTCCGGGA
GGTCTCCTACGGCTTGGAGCCATCCGGCAAGTGGCACCATCGGAACAGCTACTCTTCCTGCTAT
GCCGCGGCCGACGAGCTTATGCACCGGGAGTGCCTTCCTCCTTCCACAGTCACTGAGATCCTCA
TGAAAAACGAAGGTTCCTACGGCAGCCACCACCACCCCAGCGCCCCACATGCTGCCCCCGCCGG
GTTTTACTCTTCAGTCAACAAGAACAGCGTCCTGCCTCAAGCCTTCGACCGTTTCTTCGACAAC
GCCTACTGCGGTGGCGGCGACGCGCCCGCCGAGCCCCCCTGCTCCGGCAAGGGCGAGGCCAAGG
GGGAGCCAGAAGCGCCCCCGGCCTCGGGACTGGCGTCCCGGGCTGAGGCGGGGGCCGAGGCGGA
GGCCGAGGAGGAGAACACGAATCCCAGCTCGTCCGGTTCTGCCCACTCGGCGACCAAGGAGCCG
GCCAAGGGAGCCGCCCCCAACGCCCCCCGCACCCGCAAGAAGCGCTGCCCTTATTCGAAATTCC
AGATCCGGGAACTGGAGCGAGAGTTTTTCTTCAACGTGTATATCAACAAAGAGAAGCGGCTGCA
GCTGTCTCGGATGCTGAACCTGACGGACCGACAAGTGAAAATTTGGTTTCAGAACAGGAGGATG
AAAGAAAAAAAACTAAGCAGAGACCGGCTGCAGTATTTTTCGGGAAATCCGCTGCTGTAACTGC
AGACCGGGGGCCCTTTTGGGGGGGGGAGGGAGGGAAAGGGAGAAATTATTTTATTTTATTTTTA
TTTTTTATTTTCTAACTCGTCTTTTTTCCGCGGGTGGAAAACTGGACTGGCCAGGGCTGGCCCC
CACCGCCGTTGC

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Protein Sequences


Protein RefSeqs	XP_005325120	(Get FASTA)	NCBI Sequence Viewer
Ensembl Protein	ENSSTOP00000019763.1
GenBank Protein	KAG3291805	(Get FASTA)	NCBI Sequence Viewer

RefSeq Acc Id:

XP_005325120 ⟸ XM_005325063

- UniProtKB:

I3N5W7 (UniProtKB/TrEMBL)

- Sequence:

show sequence

MFNSVNLGNFCSPSRKERGADFGERGSCASNLYLPSCTYYVPEFSTVSSFLPQAPSRQISYPYS
AQVPPVREVSYGLEPSGKWHHRNSYSSCYAAADELMHRECLPPSTVTEILMKNEGSYGSHHHPS
APHAAPAGFYSSVNKNSVLPQAFDRFFDNAYCGGGDAPAEPPCSGKGEAKGEPEAPPASGLASR
AEAGAEAEAEEENTNPSSSGSAHSATKEPAKGAAPNAPRTRKKRCPYSKFQIRELEREFFFNVY
INKEKRLQLSRMLNLTDRQVKIWFQNRRMKEKKLSRDRLQYFSGNPLL

hide sequence

Ensembl Acc Id:

ENSSTOP00000019763 ⟸ ENSSTOT00000027675

Protein Domains

Homeobox

Additional Information

External Database Links

Database	Acc Id	Source(s)
Ensembl Genes	ENSSTOG00000028958	Ensembl, UniProtKB/TrEMBL
Ensembl Transcript	ENSSTOT00000027675.2	UniProtKB/TrEMBL
Gene3D-CATH	Homeodomain-like	UniProtKB/TrEMBL
InterPro	DUF3528	UniProtKB/TrEMBL
	Homeobox-like_sf	UniProtKB/TrEMBL
	Homeobox_CS	UniProtKB/TrEMBL
	Homeobox_dom	UniProtKB/TrEMBL
	Homeobox_metazoa	UniProtKB/TrEMBL
NCBI Gene	Hoxc11	ENTREZGENE
PANTHER	HOMEOBOX PROTEIN HOX-A11-RELATED	UniProtKB/TrEMBL
	HOMEOBOX PROTEIN HOX-C11	UniProtKB/TrEMBL
Pfam	DUF3528	UniProtKB/TrEMBL
	Homeodomain	UniProtKB/TrEMBL
PRINTS	HOMEOBOX	UniProtKB/TrEMBL
PROSITE	HOMEOBOX_1	UniProtKB/TrEMBL
	HOMEOBOX_2	UniProtKB/TrEMBL
SMART	HOX	UniProtKB/TrEMBL
Superfamily-SCOP	SSF46689	UniProtKB/TrEMBL
UniProt	I3N5W7	ENTREZGENE, UniProtKB/TrEMBL

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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