HOXC8 (homeobox C8) - Rat Genome Database

Name: HOXC8
Creator: Rat Genome Database
License: Creative Commons CC BY 4.0
Keywords: Rat Gene RGD Genome

Gene: HOXC8 (homeobox C8) Homo sapiens

Analyze

Symbol:

HOXC8

Name:

homeobox C8

RGD ID:

1353627

HGNC Page

HGNC:5129

Description:

Enables sequence-specific double-stranded DNA binding activity. Predicted to be involved in regulation of transcription by RNA polymerase II. Predicted to act upstream of or within several processes, including anterior/posterior pattern specification; negative regulation of transcription by RNA polymerase II; and skeletal system morphogenesis. Located in microtubule cytoskeleton and nucleoplasm.

Type:

protein-coding

RefSeq Status:

REVIEWED

Previously known as:

homeo box 3A; homeo box C8; homeobox protein Hox-3A; homeobox protein Hox-C8; Hox-3.1, mouse, homolog of; HOX3; HOX3A

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 ...
Mus musculus (house mouse):	Hoxc8 (homeobox C8)	HGNC	EggNOG, Ensembl, HGNC, HomoloGene, Inparanoid, NCBI, OMA, OrthoDB, OrthoMCL, PhylomeDB, Treefam
Rattus norvegicus (Norway rat):	Hoxc8 (homeobox C8)	HGNC	Ensembl, HomoloGene, NCBI, OMA, OrthoDB, OrthoMCL, PhylomeDB, Treefam
Chinchilla lanigera (long-tailed chinchilla):	Hoxc8 (homeobox C8)	NCBI	Ortholog
Pan paniscus (bonobo/pygmy chimpanzee):	HOXC8 (homeobox C8)	NCBI	Ortholog
Canis lupus familiaris (dog):	HOXC8 (homeobox C8)	HGNC	HomoloGene
Ictidomys tridecemlineatus (thirteen-lined ground squirrel):	Hoxc8 (homeobox C8)	NCBI	Ortholog
Sus scrofa (pig):	HOXC8 (homeobox C8)	HGNC	Ensembl, NCBI, OrthoDB
Chlorocebus sabaeus (green monkey):	HOXC8 (homeobox C8)	NCBI	Ortholog
Heterocephalus glaber (naked mole-rat):	Hoxc8 (homeobox C8)	NCBI	Ortholog
Other homologs ²
Mus musculus (house mouse):	Hoxb8 (homeobox B8)	HGNC	OrthoDB
Rattus norvegicus (Norway rat):	Hoxb8 (homeo box B8)	HGNC	OrthoDB
Mus musculus (house mouse):	Hoxd8 (homeobox D8)	HGNC	OrthoDB
Canis lupus familiaris (dog):	HOXB8 (homeobox B8)	HGNC	OrthoDB
Alliance orthologs ³
Rattus norvegicus (Norway rat):	Hoxc8 (homeobox C8)	Alliance	DIOPT (Ensembl Compara\|HGNC\|OrthoFinder\|OrthoInspector\|PhylomeDB\|SonicParanoid)
Mus musculus (house mouse):	Hoxc8 (homeobox C8)	Alliance	DIOPT (Ensembl Compara\|HGNC\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Danio rerio (zebrafish):	hoxc8a (homeobox C8a)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid\|ZFIN)
Drosophila melanogaster (fruit fly):	Antp	Alliance	DIOPT (Ensembl Compara\|InParanoid\|OrthoFinder)
Caenorhabditis elegans (roundworm):	mab-5	Alliance	DIOPT (Ensembl Compara\|InParanoid\|OrthoFinder\|PhylomeDB)
Xenopus tropicalis (tropical clawed frog):	hoxc8	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Xenopus laevis (African clawed frog):	hoxc8.S	Alliance	DIOPT (Xenbase)

Allele / Splice:

See ClinVar data

Latest Assembly:

GRCh38 - Human Genome Assembly GRCh38

Position:

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38	12	54,008,985 - 54,012,769 (+)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh38.p14 Ensembl	12	54,008,985 - 54,012,769 (+)	Ensembl	GRCh38		hg38	GRCh38
GRCh37	12	54,402,769 - 54,406,553 (+)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	12	52,689,157 - 52,692,814 (+)	NCBI	NCBI36	Build 36	hg18	NCBI36
Build 34	12	52,689,156 - 52,692,810	NCBI
Celera	12	54,052,507 - 54,056,164 (+)	NCBI		Celera
Cytogenetic Map	12	q13.13	NCBI
HuRef	12	51,440,618 - 51,444,277 (+)	NCBI		HuRef
CHM1_1	12	54,369,593 - 54,373,250 (+)	NCBI		CHM1_1
T2T-CHM13v2.0	12	53,960,328 - 53,978,298 (+)	NCBI		T2T-CHM13v2.0

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 (IAGP)

Gene-Chemical Interaction Annotations Click to see Annotation Detail View

17beta-estradiol (EXP)

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

aldrin (ISO)

all-trans-retinoic acid (EXP)

alpha-Zearalanol (ISO)

ammonium chloride (ISO)

arsenite(3-) (EXP)

benzo[a]pyrene (EXP)

bisphenol A (EXP,ISO)

butanal (EXP)

cadmium atom (EXP)

cadmium dichloride (EXP)

chloroethene (ISO)

chlorpyrifos (ISO)

cisplatin (EXP)

cytarabine (EXP)

lipopolysaccharide (EXP,ISO)

methylparaben (EXP)

perfluorooctanoic acid (ISO)

potassium chromate (EXP)

resveratrol (EXP)

sodium arsenite (ISO)

temozolomide (EXP)

thapsigargin (EXP)

trichloroethene (ISO)

triclosan (EXP)

troglitazone (ISO)

valproic acid (EXP,ISO)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

anterior/posterior pattern specification (IEA,ISO)

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

neuron differentiation (IEA,ISO)

regulation of DNA-templated transcription (IEA)

regulation of transcription by RNA polymerase II (IBA)

skeletal system morphogenesis (IEA,ISO)

Cellular Component

chromatin (ISA)

microtubule cytoskeleton (IDA)

nucleoplasm (IDA,TAS)

nucleus (IBA,IEA)

Molecular Function

DNA binding (IEA)

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

protein binding (IPI)

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

sequence-specific double-stranded DNA binding (IDA)

References

References - curated

#	Reference Title	Reference Citation
1.	GOAs Human GO annotations	GOA_HUMAN data from the GO Consortium
2.	Data Import for Chemical-Gene Interactions	RGD automated import pipeline for gene-chemical interactions

Additional References at PubMed

PMID:1358459	PMID:1973146	PMID:2574852	PMID:2576652	PMID:2878432	PMID:2885844	PMID:2886047	PMID:8104467	PMID:8646877	PMID:9111364	PMID:9357979	PMID:10224145
PMID:10617598	PMID:10722652	PMID:11139569	PMID:11551904	PMID:11813208	PMID:11857506	PMID:12477932	PMID:12925734	PMID:14973489	PMID:15489334	PMID:15960974	PMID:16637071
PMID:17474147	PMID:19274049	PMID:20736365	PMID:21047772	PMID:21712827	PMID:21873635	PMID:24525058	PMID:24810778	PMID:24817935	PMID:25745994	PMID:26090721	PMID:26123838
PMID:26763553	PMID:27107012	PMID:27651160	PMID:27658780	PMID:28202042	PMID:28473536	PMID:28514442	PMID:31202850	PMID:31264274	PMID:32246725	PMID:32296183	PMID:32772270
PMID:32877504	PMID:33961781	PMID:34763232	PMID:35013218	PMID:36308681	PMID:36949045	PMID:37499664	PMID:37689310	PMID:38348790	PMID:38531796	PMID:38641828

Genomics

Comparative Map Data

HOXC8
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38	12	54,008,985 - 54,012,769 (+)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh38.p14 Ensembl	12	54,008,985 - 54,012,769 (+)	Ensembl	GRCh38		hg38	GRCh38
GRCh37	12	54,402,769 - 54,406,553 (+)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	12	52,689,157 - 52,692,814 (+)	NCBI	NCBI36	Build 36	hg18	NCBI36
Build 34	12	52,689,156 - 52,692,810	NCBI
Celera	12	54,052,507 - 54,056,164 (+)	NCBI		Celera
Cytogenetic Map	12	q13.13	NCBI
HuRef	12	51,440,618 - 51,444,277 (+)	NCBI		HuRef
CHM1_1	12	54,369,593 - 54,373,250 (+)	NCBI		CHM1_1
T2T-CHM13v2.0	12	53,960,328 - 53,978,298 (+)	NCBI		T2T-CHM13v2.0

Hoxc8
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	15	102,898,971 - 102,902,707 (+)	NCBI	GRCm39	GRCm39	mm39
GRCm39 Ensembl	15	102,899,039 - 102,902,543 (+)	Ensembl		GRCm39 Ensembl
GRCm38	15	102,990,539 - 102,994,275 (+)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	15	102,990,607 - 102,994,111 (+)	Ensembl	GRCm38		mm10	GRCm38
MGSCv37	15	102,820,970 - 102,824,685 (+)	NCBI	GRCm37	MGSCv37	mm9	NCBIm37
MGSCv36	15	102,818,573 - 102,821,404 (+)	NCBI		MGSCv36	mm8
Celera	15	105,151,461 - 105,155,164 (+)	NCBI		Celera
Cytogenetic Map	15	F3	NCBI
cM Map	15	58.05	NCBI

Hoxc8
(Rattus norvegicus - Norway rat)

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCr8	7	136,006,407 - 136,008,973 (+)	NCBI		GRCr8
mRatBN7.2	7	134,127,937 - 134,130,503 (+)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	7	134,127,913 - 134,130,503 (+)	Ensembl		mRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx	7	135,883,327 - 135,885,892 (+)	NCBI	Rnor_SHR	UTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0	7	138,112,704 - 138,115,269 (+)	NCBI	Rnor_SHRSP	UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0	7	138,098,652 - 138,101,223 (+)	NCBI	Rnor_WKY	UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0	7	144,605,072 - 144,607,639 (+)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	7	144,605,058 - 144,608,538 (+)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	7	142,396,429 - 142,398,996 (+)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
Celera	7	130,553,925 - 130,556,402 (+)	NCBI		Celera
Cytogenetic Map	7	q36	NCBI

Hoxc8
(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	1,267,247 - 1,272,690 (+)	Ensembl	ChiLan1.0
ChiLan1.0	NW_004955458	1,267,247 - 1,271,354 (+)	NCBI	ChiLan1.0	ChiLan1.0

HOXC8
(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	40,173,187 - 40,180,313 (-)	NCBI		NHGRI_mPanPan1-v2
NHGRI_mPanPan1	12	40,169,953 - 40,173,734 (-)	NCBI		NHGRI_mPanPan1
Mhudiblu_PPA_v0	12	34,742,674 - 34,746,451 (-)	NCBI	Mhudiblu_PPA_v0	Mhudiblu_PPA_v0	panPan3
PanPan1.1	12	35,531,176 - 35,534,420 (-)	NCBI	panpan1.1	PanPan1.1	panPan2
PanPan1.1 Ensembl	12	35,531,200 - 35,534,420 (-)	Ensembl	panpan1.1		panPan2

HOXC8
(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	1,251,314 - 1,262,809 (-)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1
Dog10K_Boxer_Tasha	27	44,996,515 - 44,999,967 (+)	NCBI		Dog10K_Boxer_Tasha
ROS_Cfam_1.0	27	1,253,300 - 1,256,754 (-)	NCBI		ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl	27	1,254,553 - 1,256,700 (-)	Ensembl		ROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1	27	1,271,025 - 1,274,474 (-)	NCBI		UMICH_Zoey_3.1
UNSW_CanFamBas_1.0	27	1,252,555 - 1,256,007 (-)	NCBI		UNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0	27	45,400,137 - 45,403,590 (+)	NCBI		UU_Cfam_GSD_1.0

Hoxc8
(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	61,929,891 - 61,933,369 (-)	NCBI		HiC_Itri_2
SpeTri2.0 Ensembl	NW_004936512	11,231,467 - 11,234,496 (+)	Ensembl	SpeTri2.0	SpeTri2.0 Ensembl
SpeTri2.0	NW_004936512	11,231,467 - 11,234,515 (+)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

HOXC8
(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	19,222,057 - 19,225,835 (+)	Ensembl	Sscrofa11.1		susScr11	Sscrofa11.1
Sscrofa11.1	5	19,222,124 - 19,225,734 (+)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1
Sscrofa10.2	5	19,677,573 - 19,684,240 (-)	NCBI	Sscrofa10.2	Sscrofa10.2	susScr3

HOXC8
(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	50,119,515 - 50,123,276 (+)	NCBI	ChlSab1.1	ChlSab1.1	chlSab2
ChlSab1.1 Ensembl	11	50,119,932 - 50,123,411 (+)	Ensembl	ChlSab1.1	ChlSab1.1 Ensembl	chlSab2
Vero_WHO_p1.0	NW_023666037	195,918,803 - 195,926,317 (-)	NCBI	Vero_WHO_p1.0	Vero_WHO_p1.0

Hoxc8
(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	2,063,841 - 2,067,430 (+)	Ensembl	HetGla_female_1.0	HetGla_female_1.0 Ensembl	hetGla2
HetGla 1.0	NW_004624904	2,063,884 - 2,067,040 (+)	NCBI	HetGla_female_1.0	HetGla 1.0	hetGla2

Variants

Variants in HOXC8
9 total Variants

Clinical Variants

Name	Type	Condition(s)	Position(s)	Clinical significance
GRCh38/hg38 12q13.13(chr12:53224024-54222450)x1	copy number loss	See cases [RCV000052812]	Chr12:53224024..54222450 [GRCh38] Chr12:53617808..54616234 [GRCh37] Chr12:51904075..52902501 [NCBI36] Chr12:12q13.13	pathogenic
GRCh38/hg38 12p13.33-q24.33(chr12:121271-133196807)x3	copy number gain	See cases [RCV000139555]	Chr12:121271..133196807 [GRCh38] Chr12:282465..133773393 [GRCh37] Chr12:100698..132283466 [NCBI36] Chr12:12p13.33-q24.33	pathogenic
GRCh38/hg38 12q13.13(chr12:53841686-54136856)x3	copy number gain	See cases [RCV000141162]	Chr12:53841686..54136856 [GRCh38] Chr12:54235470..54530640 [GRCh37] Chr12:52521737..52816907 [NCBI36] Chr12:12q13.13	likely benign
GRCh38/hg38 12q13.13-13.3(chr12:53420606-56202942)x3	copy number gain	See cases [RCV000141435]	Chr12:53420606..56202942 [GRCh38] Chr12:53814390..56596726 [GRCh37] Chr12:52100657..54882993 [NCBI36] Chr12:12q13.13-13.3	pathogenic
GRCh37/hg19 12p13.33-q24.33(chr12:1-133851895)x3	copy number gain	See cases [RCV000258805]	Chr12:1..133851895 [GRCh37] Chr12:12p13.33-q24.33	pathogenic\|likely pathogenic
GRCh37/hg19 12p13.33-q24.33(chr12:173787-133777902)x3	copy number gain	See cases [RCV000510482]	Chr12:173787..133777902 [GRCh37] Chr12:12p13.33-q24.33	pathogenic
GRCh37/hg19 12p13.33-q24.33(chr12:173787-133777902)	copy number gain	See cases [RCV000511643]	Chr12:173787..133777902 [GRCh37] Chr12:12p13.33-q24.33	pathogenic
GRCh37/hg19 12p13.33-q24.33(chr12:191619-133777645)x3	copy number gain	not provided [RCV000750246]	Chr12:191619..133777645 [GRCh37] Chr12:12p13.33-q24.33	pathogenic
GRCh37/hg19 12p13.33-q24.33(chr12:621220-133779118)x3	copy number gain	not provided [RCV000750253]	Chr12:621220..133779118 [GRCh37] Chr12:12p13.33-q24.33	pathogenic
Single allele	deletion	Neurodevelopmental disorder [RCV000787381]	Chr12:53784698..54741363 [GRCh37] Chr12:12q13.13	pathogenic
NM_022658.4(HOXC8):c.79C>G (p.Arg27Gly)	single nucleotide variant	not specified [RCV004299831]	Chr12:54009363 [GRCh38] Chr12:54403147 [GRCh37] Chr12:12q13.13	uncertain significance
NM_022658.4(HOXC8):c.332A>C (p.Tyr111Ser)	single nucleotide variant	not specified [RCV004118750]	Chr12:54009616 [GRCh38] Chr12:54403400 [GRCh37] Chr12:12q13.13	uncertain significance
NM_022658.4(HOXC8):c.131G>T (p.Gly44Val)	single nucleotide variant	not specified [RCV004178518]	Chr12:54009415 [GRCh38] Chr12:54403199 [GRCh37] Chr12:12q13.13	uncertain significance
NM_022658.4(HOXC8):c.46G>A (p.Gly16Ser)	single nucleotide variant	not specified [RCV004262174]	Chr12:54009330 [GRCh38] Chr12:54403114 [GRCh37] Chr12:12q13.13	uncertain significance
NM_022658.4(HOXC8):c.115G>C (p.Val39Leu)	single nucleotide variant	not specified [RCV004250290]	Chr12:54009399 [GRCh38] Chr12:54403183 [GRCh37] Chr12:12q13.13	uncertain significance
NM_022658.4(HOXC8):c.80G>T (p.Arg27Leu)	single nucleotide variant	not specified [RCV004256004]	Chr12:54009364 [GRCh38] Chr12:54403148 [GRCh37] Chr12:12q13.13	uncertain significance
NM_022658.4(HOXC8):c.688G>A (p.Glu230Lys)	single nucleotide variant	not specified [RCV004356329]	Chr12:54011340 [GRCh38] Chr12:54405124 [GRCh37] Chr12:12q13.13	uncertain significance
NM_022658.4(HOXC8):c.334C>G (p.Pro112Ala)	single nucleotide variant	not specified [RCV004366087]	Chr12:54009618 [GRCh38] Chr12:54403402 [GRCh37] Chr12:12q13.13	uncertain significance
NM_022658.4(HOXC8):c.385T>G (p.Leu129Val)	single nucleotide variant	not specified [RCV004402083]	Chr12:54009669 [GRCh38] Chr12:54403453 [GRCh37] Chr12:12q13.13	uncertain significance
NM_022658.4(HOXC8):c.304G>T (p.Ala102Ser)	single nucleotide variant	not specified [RCV004402082]	Chr12:54009588 [GRCh38] Chr12:54403372 [GRCh37] Chr12:12q13.13	uncertain significance
NM_022658.4(HOXC8):c.233C>G (p.Ser78Trp)	single nucleotide variant	not specified [RCV004402081]	Chr12:54009517 [GRCh38] Chr12:54403301 [GRCh37] Chr12:12q13.13	uncertain significance

miRNA Target Status

Confirmed Target Of

miRNA Gene	Mature miRNA	Method Name	Result Type	Data Type	Support Type	PMID
MIR196A1	hsa-miR-196a-5p	Mirtarbase	external_info	Luciferase reporter assay//qRT-PCR//Western blot//	Functional MTI	19063684
MIR196A1	hsa-miR-196a-5p	Mirtarbase	external_info	Luciferase reporter assay//qRT-PCR//Reporter assay	Functional MTI	21077158
MIR196A1	hsa-miR-196a-5p	Mirtarbase	external_info	Immunohistochemistry//Luciferase reporter assay//q	Functional MTI	20736365
MIR196A1	hsa-miR-196a-5p	Mirtarbase	external_info	qRT-PCR//Western blot	Functional MTI	22545021
MIR196A1	hsa-miR-196a-5p	Tarbase	external_info	Reporter Gene	POSITIVE
MIR196A1	hsa-miR-196a-5p	OncomiRDB	external_info	NA	NA	21077158
MIR196A1	hsa-miR-196a-5p	OncomiRDB	external_info	NA	NA	20736365
MIR196A2	hsa-miR-196a-5p	Mirtarbase	external_info	Luciferase reporter assay//qRT-PCR//Western blot//	Functional MTI	19063684
MIR196A2	hsa-miR-196a-5p	Mirtarbase	external_info	Luciferase reporter assay//qRT-PCR//Reporter assay	Functional MTI	21077158
MIR196A2	hsa-miR-196a-5p	Mirtarbase	external_info	Immunohistochemistry//Luciferase reporter assay//q	Functional MTI	20736365
MIR196A2	hsa-miR-196a-5p	Mirtarbase	external_info	qRT-PCR//Western blot	Functional MTI	22545021
MIR196A2	hsa-miR-196a-5p	Tarbase	external_info	Reporter Gene	POSITIVE
MIR196A2	hsa-miR-196a-5p	OncomiRDB	external_info	NA	NA	21077158
MIR196A2	hsa-miR-196a-5p	OncomiRDB	external_info	NA	NA	20736365
MIR196B	hsa-miR-196b-5p	Mirtarbase	external_info	Immunohistochemistry//Luciferase reporter assay//q	Functional MTI	20736365
MIR196B	hsa-miR-196b-5p	OncomiRDB	external_info	NA	NA	20736365

Predicted Target Of

	Summary Value
Count of predictions:	1314
Count of miRNA genes:	768
Interacting mature miRNAs:	908
Transcripts:	ENST00000040584
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.

Markers in Region

Hoxc8

Human Assembly	Chr	Position (strand)	Source	JBrowse
GRCh37	12	54,405,118 - 54,405,221	UniSTS	GRCh37
Build 36	12	52,691,385 - 52,691,488	RGD	NCBI36
Celera	12	54,054,735 - 54,054,838	RGD
HuRef	12	51,442,846 - 51,442,950	UniSTS

HOXC8_2494

Human Assembly	Chr	Position (strand)	Source	JBrowse
GRCh37	12	54,405,864 - 54,406,464	UniSTS	GRCh37
Build 36	12	52,692,131 - 52,692,731	RGD	NCBI36
Celera	12	54,055,481 - 54,056,081	RGD
HuRef	12	51,443,593 - 51,444,194	UniSTS

MARC_43876-43875:1099078210:3

Human Assembly	Chr	Position (strand)	Source	JBrowse
GRCh37	12	54,405,108 - 54,406,050	UniSTS	GRCh37
Build 36	12	52,691,375 - 52,692,317	RGD	NCBI36
Celera	12	54,054,725 - 54,055,667	RGD
HuRef	12	51,442,836 - 51,443,779	UniSTS

MARC_44360-44361:1099347855:1

Human Assembly	Chr	Position (strand)	Source	JBrowse
GRCh37	12	54,401,612 - 54,402,268	UniSTS	GRCh37
Build 36	12	52,687,879 - 52,688,535	RGD	NCBI36
Celera	12	54,051,229 - 54,051,885	RGD
HuRef	12	51,439,324 - 51,439,980	UniSTS

MARC_41665-41666:1086710236:1

Human Assembly	Chr	Position (strand)	Source	JBrowse
GRCh37	12	54,403,322 - 54,404,919	UniSTS	GRCh37
Celera	12	54,052,939 - 54,054,536	UniSTS
HuRef	12	51,441,050 - 51,442,647	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

sensory system

adipose tissue

appendage

entire extraembryonic component

High

Medium

161

1650

624

569

131

303

1299

Low

458

690

511

245

2545

362

165

315

958

508

820

1488

Below cutoff

1541

1376

679

241

597

126

1003

1258

318

870

117

View RNA-SEQ Expression Data

Sequence

Nucleotide Sequences


RefSeq Transcripts	NM_022658	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_054371921	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_054371922	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	AC012531	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	AH010087	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	AK290959	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	BC053898	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	BU156590	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	BU618342	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	CH471054	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	CP068266	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	KT584338	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	X99680	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	X99681	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

RefSeq Acc Id:

ENST00000040584 ⟹ ENSP00000040584

Type:

CODING

Position:

Human Assembly	Chr	Position (strand)	Source
GRCh38.p14 Ensembl	12	54,008,985 - 54,012,769 (+)	Ensembl

RefSeq Acc Id:

NM_022658 ⟹ NP_073149

RefSeq Status:

REVIEWED

Type:

CODING

Position:

Human Assembly	Chr	Position (strand)	Source
GRCh38	12	54,008,985 - 54,012,769 (+)	NCBI
GRCh37	12	54,402,890 - 54,406,547 (+)	ENTREZGENE
Build 36	12	52,689,157 - 52,692,814 (+)	NCBI Archive
HuRef	12	51,440,618 - 51,444,277 (+)	ENTREZGENE
CHM1_1	12	54,369,593 - 54,373,250 (+)	NCBI
T2T-CHM13v2.0	12	53,974,515 - 53,978,298 (+)	NCBI

Sequence:

show sequence

AAGTGAGAGAGCGCGAGCTCTACCTACCGACAGTGAGGAGCGCCGCCGCCGCCGCCGCCGCCCG
CTCGCCGCCCGCCGCCGCCGCCGCCCGCGCCCCAGCCCCGGGAGCTCTGCTGATCCGGCCGAGC
TCAGCACCGAGGCGCCCCCCAACCTGCCCAGCCCCCAGCCCACCAGCCCAGCCCAGTCCCGGGG
AGCCAGCTGGCCTGGGGTTCGGTCCCGGGGGGAGGGGAGTTTCGGGGGTACTGGGCGGGGTACT
CGTGAGCCAGAGGGGAGGGGGCCGCGGGTTTTCATGTACCCAGCATGAGCTCCTACTTCGTCAA
CCCCCTGTTCTCCAAATACAAAGCCGGCGAGTCCCTGGAACCGGCCTATTACGACTGCCGGTTC
CCTCAGAGCGTGGGCAGGAGCCATGCGCTGGTGTACGGGCCCGGCGGCTCGGCGCCCGGCTTCC
AGCACGCTTCGCACCACGTTCAAGACTTCTTCCACCACGGCACCTCCGGCATCTCCAACTCAGG
CTACCAGCAGAACCCGTGCTCGCTTAGCTGCCACGGAGACGCCTCCAAATTCTATGGCTACGAG
GCGCTCCCCAGACAGTCCCTTTATGGGGCTCAGCAAGAGGCGAGCGTGGTGCAATATCCCGACT
GTAAATCCTCCGCCAACACTAACAGTAGCGAAGGACAAGGCCACTTAAATCAAAACTCGTCTCC
CAGCCTCATGTTTCCATGGATGAGACCCCACGCTCCGGGGAGGCGCAGTGGACGGCAAACTTAC
AGCCGGTATCAGACCTTGGAACTAGAAAAGGAGTTTCTCTTTAATCCTTATTTGACACGAAAAC
GTCGGATTGAAGTCTCTCATGCCCTGGGACTGACCGAGAGACAAGTGAAGATCTGGTTCCAGAA
CCGAAGGATGAAGTGGAAAAAGGAGAACAACAAGGATAAACTGCCGGGAGCCCGAGATGAGGAG
AAGGTGGAGGAAGAAGGAAATGAGGAAGAGGAGAAAGAAGAGGAGGAAAAGGAAGAAAACAAGG
ACTAAGCAAAAAAGAAAGACCCCCCCCCCCTTAGCAACTCCCTTGAAGTTTCGTTTTATGGTAG
CAGATAAATTGAGAAGTTTACGACTGTCATTTGCTTTTATAGAGAATAGAATGACACTCACAAC
TCTAACTACCTGTCAGATACTTGCAGCTCTGGTTTTATTACCTTTGGACTTCCCCCACTCTTTA
TTTGTTTGGGGGCTGGAGGGGGGAGACGGAGAAACAGTGAAAAGTTCGGACTCTCTGTCTCACT
CCTTGCCCCACACACACTTGTCCCTGCCCCCACCCTTCTGAGTCCTTCCTGGATTTTAAGGTCT
GAGACCTGGCCTCCGTGCTCCTCGGTCTGTCTCTCACCACACTCCCACCTCCCTGCTTCTCTGG
TATTTATTTTAGAGGGGAGCCCCCTCGAAATGCAGAAAAGGACTTGTGGTTTTGTTTTTATGCT
AAGGCTAGTGTACTAGATGTACTTTTTCTAAAAAGGAAAGGACAGAAAAAAATGAAGAAAGGAA
AGGAAGACAAATGTAAAGAAATAAGGAAAAAAGCAAGGAATATCCCCTCCCCCTCCCCCTCCCC
CTCCCCAGGGCTCCCTGCTTAGAAAAACCCCCTTGACTTTCTCTAGGAACCTGATGGAAACCTG
AAGGAGATGTGGGTCTTTCCCCTCCCCCCATTTCCAGAAGGGTAGATAGGAGCCTGCAGTCGCC
TCTAAAATCCTACCTAACCATCCCATGGTCACTCGGGCCCATGCCTTCCTCTCCTTCGCTGTTT
GATTTCTATTCTGTTGGGCCCGCCTTCCTCTGAGCTGCATTAGTGTTAGTGCTCAGAAATCACC
ATAATCACGAAAATAATAATAATAAATCTTTAACATACTACCTAAAGGGAACCTGCAATAATCT
TGAAAAAGAAAAAGAGAAAAATTTTAAAATCCTGCTATAGGAGAAAAAAAGAGAAAAAAATAAA
AATCAAAAAAAAAAAAAAGAAAGAAAGAAACCTCCAGCGTATTTTATCACTACCTATAGAAAGA
AATCCTGCTTTGAGAGTATTTGTAATGCGGTTTTGTTGTCGTTTGTTGCTGCTTATTTCACTAA
GAAAACCCAACAACTGAGACTGCCTAGCCCGCCGGTCCTGTGCGCTTTTATTGTGCTTCTAACC
CCAGTAGAGTAGAACTAAATTGCACTGAATGTATAGTTAACTCTGTCTTGAATTCTCTGTTTAT
GCAATGTGCTCGAAAGAAAAAAATGTTAAAAATATATCTATAATAATAATTTTTTGTCATTTGT
CTTTATGTCCAGCTATGAATGTAGATTTTGTGTCCCGACAGCCCTGTTCCTGGTCCAAGTACTT
TGTATTGTATACGTGAGTCATAATAATAAAAAGAAGAAGAAAAATAATA

hide sequence

RefSeq Acc Id:

XM_054371921 ⟹ XP_054227896

Type:

CODING

Position:

Human Assembly	Chr	Position (strand)	Source
T2T-CHM13v2.0	12	53,960,328 - 53,978,298 (+)	NCBI

RefSeq Acc Id:

XM_054371922 ⟹ XP_054227897

Type:

CODING

Position:

Human Assembly	Chr	Position (strand)	Source
T2T-CHM13v2.0	12	53,970,728 - 53,978,298 (+)	NCBI

Protein Sequences


Protein RefSeqs	NP_073149	(Get FASTA)	NCBI Sequence Viewer
	XP_054227896	(Get FASTA)	NCBI Sequence Viewer
	XP_054227897	(Get FASTA)	NCBI Sequence Viewer
GenBank Protein	AAG42146	(Get FASTA)	NCBI Sequence Viewer
	AAH53898	(Get FASTA)	NCBI Sequence Viewer
	BAF83648	(Get FASTA)	NCBI Sequence Viewer
	CAA67996	(Get FASTA)	NCBI Sequence Viewer
	CAA67997	(Get FASTA)	NCBI Sequence Viewer
	EAW96743	(Get FASTA)	NCBI Sequence Viewer
Ensembl Protein	ENSP00000040584
	ENSP00000040584.4
GenBank Protein	P31273	(Get FASTA)	NCBI Sequence Viewer

RefSeq Acc Id:

NP_073149 ⟸ NM_022658

- UniProtKB:

O15221 (UniProtKB/Swiss-Prot), A8K4J4 (UniProtKB/Swiss-Prot), O15362 (UniProtKB/Swiss-Prot), P31273 (UniProtKB/Swiss-Prot)

- Sequence:

show sequence

MSSYFVNPLFSKYKAGESLEPAYYDCRFPQSVGRSHALVYGPGGSAPGFQHASHHVQDFFHHGT
SGISNSGYQQNPCSLSCHGDASKFYGYEALPRQSLYGAQQEASVVQYPDCKSSANTNSSEGQGH
LNQNSSPSLMFPWMRPHAPGRRSGRQTYSRYQTLELEKEFLFNPYLTRKRRIEVSHALGLTERQ
VKIWFQNRRMKWKKENNKDKLPGARDEEKVEEEGNEEEEKEEEEKEENKD

hide sequence

RefSeq Acc Id:

ENSP00000040584 ⟸ ENST00000040584

RefSeq Acc Id:	XP_054227896 ⟸ XM_054371921
- Peptide Label:	isoform X1
- UniProtKB:	P31273 (UniProtKB/Swiss-Prot), O15221 (UniProtKB/Swiss-Prot), A8K4J4 (UniProtKB/Swiss-Prot), O15362 (UniProtKB/Swiss-Prot)

RefSeq Acc Id:	XP_054227897 ⟸ XM_054371922
- Peptide Label:	isoform X1
- UniProtKB:	P31273 (UniProtKB/Swiss-Prot), O15221 (UniProtKB/Swiss-Prot), A8K4J4 (UniProtKB/Swiss-Prot), O15362 (UniProtKB/Swiss-Prot)

Protein Structures

Name	Modeler	Protein Id	AA Range	Protein Structure
AF-P31273-F1-model_v2	AlphaFold	P31273	1-242	view protein structure

Promoters

RGD ID:

7224199

Promoter ID:

EPDNEW_H17844

Type:

initiation region

Name:

HOXC8_2

Description:

homeobox C8

SO ACC ID:

SO:0000170

Source:

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

Alternative Promoters:

null; see alsoEPDNEW_H17839 EPDNEW_H17845 EPDNEW_H17846 EPDNEW_H17847

Experiment Methods:

Single-end sequencing.; Paired-end sequencing.

Position:

Human Assembly	Chr	Position (strand)	Source
GRCh38	12	54,005,065 - 54,005,125	EPDNEW

RGD ID:

7224197

Promoter ID:

EPDNEW_H17845

Type:

initiation region

Name:

HOXC8_1

Description:

homeobox C8

SO ACC ID:

SO:0000170

Source:

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

Alternative Promoters:

null; see alsoEPDNEW_H17839 EPDNEW_H17844 EPDNEW_H17846 EPDNEW_H17847

Experiment Methods:

Single-end sequencing.

Position:

Human Assembly	Chr	Position (strand)	Source
GRCh38	12	54,009,013 - 54,009,073	EPDNEW

RGD ID:

7224201

Promoter ID:

EPDNEW_H17846

Type:

initiation region

Name:

HOXC8_3

Description:

homeobox C8

SO ACC ID:

SO:0000170

Source:

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

Alternative Promoters:

null; see alsoEPDNEW_H17839 EPDNEW_H17845 EPDNEW_H17844 EPDNEW_H17847

Experiment Methods:

Single-end sequencing.; Paired-end sequencing.

Position:

Human Assembly	Chr	Position (strand)	Source
GRCh38	12	54,009,401 - 54,009,461	EPDNEW

RGD ID:

7224203

Promoter ID:

EPDNEW_H17847

Type:

initiation region

Name:

HOXC8_5

Description:

homeobox C8

SO ACC ID:

SO:0000170

Source:

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

Alternative Promoters:

null; see alsoEPDNEW_H17839 EPDNEW_H17845 EPDNEW_H17844 EPDNEW_H17846

Experiment Methods:

Single-end sequencing.; Paired-end sequencing.

Position:

Human Assembly	Chr	Position (strand)	Source
GRCh38	12	54,011,591 - 54,011,651	EPDNEW

Additional Information

External Database Links

Database	Acc Id	Source(s)
AGR Gene	HGNC:5129	AgrOrtholog
COSMIC	HOXC8	COSMIC
Ensembl Genes	ENSG00000037965	Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript	ENST00000040584	ENTREZGENE
	ENST00000040584.6	UniProtKB/Swiss-Prot
Gene3D-CATH	Homeodomain-like	UniProtKB/Swiss-Prot
GTEx	ENSG00000037965	GTEx
HGNC ID	HGNC:5129	ENTREZGENE
Human Proteome Map	HOXC8	Human Proteome Map
InterPro	Homeobox-like_sf	UniProtKB/Swiss-Prot
	Homeobox_Antennapedia_CS	UniProtKB/Swiss-Prot
	Homeobox_CS	UniProtKB/Swiss-Prot
	Homeobox_dom	UniProtKB/Swiss-Prot
	Homeobox_metazoa	UniProtKB/Swiss-Prot
	HTH_motif	UniProtKB/Swiss-Prot
KEGG Report	hsa:3224	UniProtKB/Swiss-Prot
NCBI Gene	3224	ENTREZGENE
OMIM	142970	OMIM
PANTHER	HOMEOBOX DOMAIN-CONTAINING PROTEIN	UniProtKB/Swiss-Prot
	HOMEOBOX PROTEIN HOX-C8	UniProtKB/Swiss-Prot
Pfam	Homeodomain	UniProtKB/Swiss-Prot
PharmGKB	PA29404	PharmGKB
PRINTS	HOMEOBOX	UniProtKB/Swiss-Prot
	HTHREPRESSR	UniProtKB/Swiss-Prot
PROSITE	ANTENNAPEDIA	UniProtKB/Swiss-Prot
	HOMEOBOX_1	UniProtKB/Swiss-Prot
	HOMEOBOX_2	UniProtKB/Swiss-Prot
SMART	HOX	UniProtKB/Swiss-Prot
Superfamily-SCOP	SSF46689	UniProtKB/Swiss-Prot
UniProt	A8K4J4	ENTREZGENE
	HXC8_HUMAN	UniProtKB/Swiss-Prot
	O15221	ENTREZGENE
	O15362	ENTREZGENE
	P31273	ENTREZGENE
UniProt Secondary	A8K4J4	UniProtKB/Swiss-Prot
	O15221	UniProtKB/Swiss-Prot
	O15362	UniProtKB/Swiss-Prot

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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Imported Disease Annotations - ClinVar