HOXD11 (homeobox D11) - Rat Genome Database

Name: HOXD11
Creator: Rat Genome Database
License: Creative Commons CC BY 4.0
Keywords: Rat Gene RGD Genome

Gene: HOXD11 (homeobox D11) Homo sapiens

Analyze

Symbol:

HOXD11

Name:

homeobox D11

RGD ID:

1346896

HGNC Page

HGNC:5134

Description:

Enables sequence-specific double-stranded DNA binding activity. Predicted to be involved in branching involved in ureteric bud morphogenesis; dorsal/ventral pattern formation; and regulation of transcription by RNA polymerase II. Predicted to act upstream of or within several processes, including embryonic morphogenesis; positive regulation of chondrocyte development; and regionalization. Located in nucleoplasm.

Type:

protein-coding

RefSeq Status:

REVIEWED

Previously known as:

homeo box 4F; homeo box D11; homeobox protein Hox-4F; homeobox protein Hox-D11; Hox-4.6, mouse, homolog of; HOX4; HOX4F

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):	Hoxd11 (homeobox D11)	HGNC	EggNOG, Ensembl, HGNC, HomoloGene, Inparanoid, NCBI, OMA, OrthoDB, Panther, PhylomeDB, Treefam
Rattus norvegicus (Norway rat):	Hoxd11 (homeobox D11)	HGNC	Ensembl, NCBI
Chinchilla lanigera (long-tailed chinchilla):	Hoxd11 (homeobox D11)	NCBI	Ortholog
Pan paniscus (bonobo/pygmy chimpanzee):	HOXD11 (homeobox D11)	NCBI	Ortholog
Canis lupus familiaris (dog):	HOXD11 (homeobox D11)	HGNC	EggNOG, Ensembl, Inparanoid, NCBI, OMA, OrthoDB, OrthoMCL, Panther, Treefam
Sus scrofa (pig):	HOXD11 (homeobox D11)	HGNC	Ensembl, NCBI, OrthoDB
Chlorocebus sabaeus (green monkey):	HOXD11 (homeobox D11)	NCBI	Ortholog
Alliance orthologs ³
Mus musculus (house mouse):	Hoxd11 (homeobox D11)	Alliance	DIOPT (Ensembl Compara\|HGNC\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Rattus norvegicus (Norway rat):	Hoxd11 (homeobox D11)	Alliance	DIOPT (Ensembl Compara\|HGNC\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Danio rerio (zebrafish):	hoxd11a (homeobox D11a)	Alliance	DIOPT (Ensembl Compara\|OMA\|OrthoFinder\|PANTHER\|PhylomeDB\|ZFIN)
Drosophila melanogaster (fruit fly):	Abd-B	Alliance	DIOPT (Ensembl Compara\|OrthoFinder\|OrthoInspector)
Xenopus tropicalis (tropical clawed frog):	hoxd10	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|SonicParanoid)

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	2	176,107,280 - 176,115,679 (+)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh38.p14 Ensembl	2	176,104,216 - 176,109,754 (+)	Ensembl	GRCh38		hg38	GRCh38
GRCh37	2	176,972,008 - 176,974,482 (+)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	2	176,680,330 - 176,682,562 (+)	NCBI	NCBI36	Build 36	hg18	NCBI36
Build 34	2	176,797,590 - 176,799,823	NCBI
Celera	2	170,581,234 - 170,583,461 (+)	NCBI		Celera
Cytogenetic Map	2	q31.1	NCBI
HuRef	2	168,849,568 - 168,851,540 (+)	NCBI		HuRef
CHM1_1	2	176,977,935 - 176,980,184 (+)	NCBI		CHM1_1
T2T-CHM13v2.0	2	176,595,402 - 176,599,952 (+)	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

autistic disorder (EXP)

bone development disease (EXP)

Breast Neoplasms (EXP)

Congenital Limb Deformities (EXP)

Disease Progression (EXP)

head and neck squamous cell carcinoma (EXP)

high grade glioma (EXP)

kidney disease (EXP)

Kyphoscoliosis (ISO)

male infertility (EXP)

Mouth Neoplasms (EXP)

Ovarian Neoplasms (EXP)

rheumatoid arthritis (EXP)

split hand-foot malformation 5 (IAGP)

Gene-Chemical Interaction Annotations Click to see Annotation Detail View

1,2-dichloroethane (ISO)

17beta-hydroxy-5alpha-androstan-3-one (EXP)

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

4,4'-sulfonyldiphenol (ISO)

aflatoxin B1 (EXP)

amosite asbestos (EXP)

arsenite(3-) (EXP)

benzo[a]pyrene (EXP)

bisphenol A (ISO)

chlordecone (ISO)

chlorpyrifos (ISO)

cisplatin (EXP)

crocidolite asbestos (EXP)

entinostat (EXP)

exemestane (EXP)

flusilazole (ISO)

lipopolysaccharide (EXP)

paracetamol (EXP)

perfluorohexanesulfonic acid (ISO)

pirinixic acid (EXP)

resveratrol (EXP)

S-(1,2-dichlorovinyl)-L-cysteine (EXP)

serpentine asbestos (EXP)

sodium arsenite (ISO)

temozolomide (EXP)

tunicamycin (EXP)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

anterior/posterior pattern specification (ISO)

branching involved in ureteric bud morphogenesis (ISO,ISS)

cartilage development involved in endochondral bone morphogenesis (ISO)

cell development (ISO)

chondrocyte development (ISO)

chondrocyte differentiation (ISO)

developmental growth (ISO)

dorsal/ventral pattern formation (ISO,ISS)

embryonic digit morphogenesis (ISO)

embryonic forelimb morphogenesis (ISO)

embryonic limb morphogenesis (ISO)

embryonic skeletal joint morphogenesis (ISO)

metanephros development (ISO)

organ induction (ISO)

pattern specification process (ISO)

positive regulation of chondrocyte development (ISO)

positive regulation of chondrocyte differentiation (ISO)

proximal/distal pattern formation (ISO)

regulation of chondrocyte differentiation (ISO)

regulation of DNA-templated transcription (IEA)

regulation of gene expression (ISO)

regulation of transcription by RNA polymerase II (IBA,IEA)

single fertilization (ISO)

skeletal system development (ISO)

Cellular Component

chromatin (ISA)

nucleoplasm (IDA)

nucleus (IBA,IEA)

Molecular Function

DNA binding (IEA)

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

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

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
3.	Abnormalities of vertebral formation and Hox expression in congenital kyphoscoliotic rats.	Seki T, etal., Mol Cell Biochem. 2008 May;312(1-2):193-9. doi: 10.1007/s11010-008-9734-4. Epub 2008 Mar 9.

Additional References at PubMed

PMID:1358459	PMID:1973146	PMID:2574852	PMID:8890171	PMID:9323126	PMID:9343407	PMID:10075849	PMID:10364522	PMID:11060466	PMID:11493536	PMID:11778160	PMID:11782354
PMID:11857506	PMID:12217321	PMID:12357469	PMID:12477932	PMID:17236141	PMID:19255789	PMID:19274049	PMID:19453261	PMID:19540081	PMID:19938081	PMID:20085705	PMID:21873635
PMID:25301728	PMID:27363011	PMID:27609421	PMID:27658780	PMID:28473536	PMID:29844126	PMID:33961781	PMID:35140242	PMID:36151071	PMID:36774506	PMID:38308324

Genomics

Comparative Map Data

HOXD11
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38	2	176,107,280 - 176,115,679 (+)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh38.p14 Ensembl	2	176,104,216 - 176,109,754 (+)	Ensembl	GRCh38		hg38	GRCh38
GRCh37	2	176,972,008 - 176,974,482 (+)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	2	176,680,330 - 176,682,562 (+)	NCBI	NCBI36	Build 36	hg18	NCBI36
Build 34	2	176,797,590 - 176,799,823	NCBI
Celera	2	170,581,234 - 170,583,461 (+)	NCBI		Celera
Cytogenetic Map	2	q31.1	NCBI
HuRef	2	168,849,568 - 168,851,540 (+)	NCBI		HuRef
CHM1_1	2	176,977,935 - 176,980,184 (+)	NCBI		CHM1_1
T2T-CHM13v2.0	2	176,595,402 - 176,599,952 (+)	NCBI		T2T-CHM13v2.0

Hoxd11
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	2	74,509,902 - 74,517,360 (+)	NCBI	GRCm39	GRCm39	mm39
GRCm39 Ensembl	2	74,509,901 - 74,517,360 (+)	Ensembl		GRCm39 Ensembl
GRCm38	2	74,679,558 - 74,687,016 (+)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	2	74,679,557 - 74,687,016 (+)	Ensembl	GRCm38		mm10	GRCm38
MGSCv37	2	74,520,450 - 74,522,195 (+)	NCBI	GRCm37	MGSCv37	mm9	NCBIm37
MGSCv36	2	74,483,232 - 74,484,977 (+)	NCBI		MGSCv36	mm8
Celera	2	76,352,501 - 76,354,246 (+)	NCBI		Celera
Cytogenetic Map	2	C3	NCBI
cM Map	2	44.13	NCBI

Hoxd11
(Rattus norvegicus - Norway rat)

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCr8	3	79,992,394 - 79,994,688 (+)	NCBI		GRCr8
mRatBN7.2	3	59,584,840 - 59,587,257 (+)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	3	59,585,039 - 59,586,783 (+)	Ensembl		mRatBN7.2 Ensembl
Rnor_6.0	3	61,604,256 - 61,606,874 (+)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	3	61,604,672 - 61,606,400 (+)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	3	68,071,282 - 68,076,686 (+)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
Celera	3	59,104,507 - 59,109,071 (+)	NCBI		Celera
Cytogenetic Map	3	q23	NCBI

Hoxd11
(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	NW_004955403	20,541,870 - 20,556,574 (-)	NCBI	ChiLan1.0	ChiLan1.0

HOXD11
(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	13	78,774,821 - 78,780,697 (+)	NCBI		NHGRI_mPanPan1-v2
NHGRI_mPanPan1	2B	78,789,797 - 78,792,163 (+)	NCBI		NHGRI_mPanPan1
Mhudiblu_PPA_v0	2B	63,386,806 - 63,398,777 (+)	NCBI	Mhudiblu_PPA_v0	Mhudiblu_PPA_v0	panPan3
PanPan1.1	2B	181,095,347 - 181,098,680 (+)	NCBI	panpan1.1	PanPan1.1	panPan2

HOXD11
(Canis lupus familiaris - dog)

Dog Assembly	Chr	Position (strand)	Source	Genome Browsers
Dog Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
CanFam3.1	36	19,913,064 - 19,926,868 (+)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1
CanFam3.1 Ensembl	36	19,914,431 - 19,916,766 (+)	Ensembl	CanFam3.1		canFam3	CanFam3.1
Dog10K_Boxer_Tasha	36	19,921,364 - 19,929,032 (+)	NCBI		Dog10K_Boxer_Tasha
ROS_Cfam_1.0	36	20,052,553 - 20,060,228 (+)	NCBI		ROS_Cfam_1.0
UMICH_Zoey_3.1	36	20,129,998 - 20,134,442 (+)	NCBI		UMICH_Zoey_3.1
UNSW_CanFamBas_1.0	36	20,130,689 - 20,135,144 (+)	NCBI		UNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0	36	20,239,278 - 20,246,796 (+)	NCBI		UU_Cfam_GSD_1.0

HOXD11
(Sus scrofa - pig)

Pig Assembly	Chr	Position (strand)	Source	Genome Browsers
Pig Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Sscrofa11.1 Ensembl	15	81,908,460 - 81,911,282 (+)	Ensembl	Sscrofa11.1		susScr11	Sscrofa11.1
Sscrofa11.1	15	81,906,654 - 81,910,765 (+)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1
Sscrofa10.2	15	91,374,469 - 91,377,543 (+)	NCBI	Sscrofa10.2	Sscrofa10.2	susScr3

HOXD11
(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	10	61,681,474 - 61,693,974 (+)	NCBI	ChlSab1.1	ChlSab1.1	chlSab2
ChlSab1.1 Ensembl	10	61,682,400 - 61,684,168 (+)	Ensembl	ChlSab1.1	ChlSab1.1 Ensembl	chlSab2
Vero_WHO_p1.0	NW_023666040	137,925,780 - 137,928,157 (-)	NCBI	Vero_WHO_p1.0	Vero_WHO_p1.0

Variants

Variants in HOXD11
23 total Variants

Clinical Variants

Name	Type	Condition(s)	Position(s)	Clinical significance
GRCh38/hg38 2q31.1-33.2(chr2:174898848-203941548)x1	copy number loss	See cases [RCV000050980]	Chr2:174898848..203941548 [GRCh38] Chr2:175763576..204806271 [GRCh37] Chr2:175471822..204514516 [NCBI36] Chr2:2q31.1-33.2	pathogenic
GRCh38/hg38 2q31.1-31.2(chr2:172779876-177598000)x1	copy number loss	See cases [RCV000050765]	Chr2:172779876..177598000 [GRCh38] Chr2:173644604..178462728 [GRCh37] Chr2:173352850..178170974 [NCBI36] Chr2:2q31.1-31.2	pathogenic
GRCh38/hg38 2q31.1(chr2:172366752-176361187)x1	copy number loss	See cases [RCV000052554]	Chr2:172366752..176361187 [GRCh38] Chr2:173231480..177225915 [GRCh37] Chr2:172939726..176934161 [NCBI36] Chr2:2q31.1	pathogenic
GRCh38/hg38 2q31.1-31.2(chr2:173408061-177702487)x1	copy number loss	See cases [RCV000052555]	Chr2:173408061..177702487 [GRCh38] Chr2:174272789..178567215 [GRCh37] Chr2:173981035..178275461 [NCBI36] Chr2:2q31.1-31.2	pathogenic
GRCh38/hg38 2q24.3-32.1(chr2:163965382-182195062)x1	copy number loss	See cases [RCV000054122]	Chr2:163965382..182195062 [GRCh38] Chr2:164821892..183059789 [GRCh37] Chr2:164530138..182768034 [NCBI36] Chr2:2q24.3-32.1	pathogenic
GRCh38/hg38 2q31.1-32.1(chr2:170407688-186189894)x1	copy number loss	See cases [RCV000054127]	Chr2:170407688..186189894 [GRCh38] Chr2:171264198..187054621 [GRCh37] Chr2:170972444..186762866 [NCBI36] Chr2:2q31.1-32.1	pathogenic
GRCh38/hg38 2q31.1-32.2(chr2:171429233-189179568)x1	copy number loss	See cases [RCV000136850]	Chr2:171429233..189179568 [GRCh38] Chr2:172285743..190044294 [GRCh37] Chr2:171993989..189752539 [NCBI36] Chr2:2q31.1-32.2	pathogenic
GRCh38/hg38 2q31.1-32.2(chr2:174634502-189000964)x1	copy number loss	See cases [RCV000136861]	Chr2:174634502..189000964 [GRCh38] Chr2:175499230..189865690 [GRCh37] Chr2:175207476..189573935 [NCBI36] Chr2:2q31.1-32.2	pathogenic
GRCh38/hg38 2q31.1(chr2:176090995-176108288)x3	copy number gain	See cases [RCV000136650]	Chr2:176090995..176108288 [GRCh38] Chr2:176955723..176973016 [GRCh37] Chr2:176663969..176681262 [NCBI36] Chr2:2q31.1	uncertain significance
GRCh38/hg38 2q31.1(chr2:176075289-176156257)x1	copy number loss	See cases [RCV000137847]	Chr2:176075289..176156257 [GRCh38] Chr2:176940017..177020985 [GRCh37] Chr2:176648263..176729231 [NCBI36] Chr2:2q31.1	pathogenic
GRCh38/hg38 2q31.1-31.2(chr2:171513047-177854080)x1	copy number loss	See cases [RCV000139646]	Chr2:171513047..177854080 [GRCh38] Chr2:172369557..178718807 [GRCh37] Chr2:172077803..178427053 [NCBI36] Chr2:2q31.1-31.2	pathogenic
GRCh38/hg38 2q31.1-31.3(chr2:174236451-181188846)x1	copy number loss	See cases [RCV000143597]	Chr2:174236451..181188846 [GRCh38] Chr2:175101179..182053573 [GRCh37] Chr2:174809425..181761818 [NCBI36] Chr2:2q31.1-31.3	pathogenic
GRCh38/hg38 2q31.1-32.3(chr2:176086763-193201970)x1	copy number loss	See cases [RCV000143484]	Chr2:176086763..193201970 [GRCh38] Chr2:176951491..194066696 [GRCh37] Chr2:176659737..193774941 [NCBI36] Chr2:2q31.1-32.3	pathogenic
GRCh37/hg19 2q24.1-31.3(chr2:156489430-182921298)x3	copy number gain	See cases [RCV000239848]	Chr2:156489430..182921298 [GRCh37] Chr2:2q24.1-31.3	pathogenic
GRCh37/hg19 2q31.1-35(chr2:169829974-215521436)x3	copy number gain	See cases [RCV000448271]	Chr2:169829974..215521436 [GRCh37] Chr2:2q31.1-35	pathogenic
GRCh37/hg19 2p25.3-q37.3(chr2:12771-242783384)	copy number gain	See cases [RCV000512056]	Chr2:12771..242783384 [GRCh37] Chr2:2p25.3-q37.3	pathogenic
GRCh37/hg19 2p25.3-q37.3(chr2:12771-242783384)x3	copy number gain	See cases [RCV000511212]	Chr2:12771..242783384 [GRCh37] Chr2:2p25.3-q37.3	pathogenic
GRCh37/hg19 2q31.1(chr2:175887486-176989647)x1	copy number loss	See cases [RCV000515569]	Chr2:175887486..176989647 [GRCh37] Chr2:2q31.1	pathogenic
GRCh37/hg19 2q31.1-31.2(chr2:173741558-178416381)x1	copy number loss	not provided [RCV000682153]	Chr2:173741558..178416381 [GRCh37] Chr2:2q31.1-31.2	pathogenic
GRCh37/hg19 2p25.3-q37.3(chr2:15672-243101834)x3	copy number gain	not provided [RCV000752804]	Chr2:15672..243101834 [GRCh37] Chr2:2p25.3-q37.3	pathogenic
GRCh37/hg19 2p25.3-q37.3(chr2:14238-243048760)x3	copy number gain	not provided [RCV000752802]	Chr2:14238..243048760 [GRCh37] Chr2:2p25.3-q37.3	pathogenic
GRCh37/hg19 2q23.3-31.2(chr2:152409978-179325736)x3	copy number gain	not provided [RCV000740654]	Chr2:152409978..179325736 [GRCh37] Chr2:2q23.3-31.2	pathogenic
GRCh37/hg19 2q31.1-31.3(chr2:174238257-181604341)x1	copy number loss	not provided [RCV000740710]	Chr2:174238257..181604341 [GRCh37] Chr2:2q31.1-31.3	pathogenic
GRCh37/hg19 2q31.1(chr2:176950926-177047801)x3	copy number gain	not provided [RCV000740716]	Chr2:176950926..177047801 [GRCh37] Chr2:2q31.1	benign
GRCh37/hg19 2q31.1(chr2:176951487-177070756)x3	copy number gain	not provided [RCV000740717]	Chr2:176951487..177070756 [GRCh37] Chr2:2q31.1	benign
NM_021192.3(HOXD11):c.804A>G (p.Lys268=)	single nucleotide variant	not provided [RCV000946652]	Chr2:176108929 [GRCh38] Chr2:176973657 [GRCh37] Chr2:2q31.1	likely benign
GRCh37/hg19 2q31.1-31.2(chr2:176794846-178494259)	copy number loss	not provided [RCV000767781]	Chr2:176794846..178494259 [GRCh37] Chr2:2q31.1-31.2	pathogenic
GRCh37/hg19 2q31.1-31.2(chr2:176310551-179092634)x1	copy number loss	not provided [RCV000849015]	Chr2:176310551..179092634 [GRCh37] Chr2:2q31.1-31.2	pathogenic
GRCh37/hg19 2q31.1-32.3(chr2:174690039-195521582)x1	copy number loss	not provided [RCV001005359]	Chr2:174690039..195521582 [GRCh37] Chr2:2q31.1-32.3	pathogenic
GRCh37/hg19 2q24.3-32.3(chr2:167329586-192756373)x1	copy number loss	not provided [RCV000848216]	Chr2:167329586..192756373 [GRCh37] Chr2:2q24.3-32.3	pathogenic
GRCh37/hg19 2q31.1-32.1(chr2:173538954-186401606)x1	copy number loss	not provided [RCV000846537]	Chr2:173538954..186401606 [GRCh37] Chr2:2q31.1-32.1	pathogenic
GRCh37/hg19 2q24.2-34(chr2:163233162-211927188)x3	copy number gain	not provided [RCV001005349]	Chr2:163233162..211927188 [GRCh37] Chr2:2q24.2-34	pathogenic
NM_021192.3(HOXD11):c.879A>G (p.Lys293=)	single nucleotide variant	not provided [RCV000887655]	Chr2:176109004 [GRCh38] Chr2:176973732 [GRCh37] Chr2:2q31.1	benign
NM_021192.3(HOXD11):c.954G>A (p.Arg318=)	single nucleotide variant	not provided [RCV000974437]	Chr2:176109079 [GRCh38] Chr2:176973807 [GRCh37] Chr2:2q31.1	benign
GRCh37/hg19 2q24.2-31.3(chr2:163078055-182119617)x1	copy number loss	2q24 microdeletion syndrome [RCV001263223]	Chr2:163078055..182119617 [GRCh37] Chr2:2q24.2-31.3	pathogenic
GRCh37/hg19 2p25.3-q37.3(chr2:1-243199373)	copy number gain	Mosaic trisomy 2 [RCV002280628]	Chr2:1..243199373 [GRCh37] Chr2:2p25.3-q37.3	pathogenic
GRCh37/hg19 2q31.1-31.3(chr2:171999572-182774361)	copy number loss	3-4 finger syndactyly [RCV001352646]	Chr2:171999572..182774361 [GRCh37] Chr2:2q31.1-31.3	pathogenic
GRCh37/hg19 2q31.1(chr2:174673094-177275625)x3	copy number gain	not provided [RCV001825257]	Chr2:174673094..177275625 [GRCh37] Chr2:2q31.1	not provided
GRCh37/hg19 2q31.1-35(chr2:169829974-215521436)	copy number gain	not specified [RCV002053265]	Chr2:169829974..215521436 [GRCh37] Chr2:2q31.1-35	pathogenic
NC_000002.11:g.(?_176957619)_(176973870_?)del	deletion	not provided [RCV003111345]	Chr2:176957619..176973870 [GRCh37] Chr2:2q31.1	pathogenic
Single allele	deletion	Split hand-foot malformation 5 [RCV002264898]	Chr2:171524396..178694337 [GRCh37] Chr2:2q31.1-31.2	pathogenic
GRCh37/hg19 2q31.1-31.3(chr2:175143352-180999636)x1	copy number loss	not provided [RCV002474570]	Chr2:175143352..180999636 [GRCh37] Chr2:2q31.1-31.3	pathogenic
NM_021192.3(HOXD11):c.500C>A (p.Ala167Glu)	single nucleotide variant	not specified [RCV004147489]	Chr2:176107855 [GRCh38] Chr2:176972583 [GRCh37] Chr2:2q31.1	uncertain significance
NM_021192.3(HOXD11):c.613G>A (p.Glu205Lys)	single nucleotide variant	not specified [RCV004198147]	Chr2:176107968 [GRCh38] Chr2:176972696 [GRCh37] Chr2:2q31.1	uncertain significance
NM_021192.3(HOXD11):c.233G>A (p.Gly78Asp)	single nucleotide variant	not specified [RCV004178320]	Chr2:176107588 [GRCh38] Chr2:176972316 [GRCh37] Chr2:2q31.1	uncertain significance
NM_021192.3(HOXD11):c.740G>A (p.Gly247Asp)	single nucleotide variant	not specified [RCV004077447]	Chr2:176108095 [GRCh38] Chr2:176972823 [GRCh37] Chr2:2q31.1	uncertain significance
NM_021192.3(HOXD11):c.670C>A (p.Pro224Thr)	single nucleotide variant	not specified [RCV004186732]	Chr2:176108025 [GRCh38] Chr2:176972753 [GRCh37] Chr2:2q31.1	uncertain significance
NM_021192.3(HOXD11):c.949C>T (p.Arg317Cys)	single nucleotide variant	not specified [RCV004220828]	Chr2:176109074 [GRCh38] Chr2:176973802 [GRCh37] Chr2:2q31.1	uncertain significance
NM_021192.3(HOXD11):c.95C>G (p.Pro32Arg)	single nucleotide variant	not specified [RCV004180069]	Chr2:176107450 [GRCh38] Chr2:176972178 [GRCh37] Chr2:2q31.1	uncertain significance
NM_021192.3(HOXD11):c.763G>A (p.Glu255Lys)	single nucleotide variant	not specified [RCV004162861]	Chr2:176108118 [GRCh38] Chr2:176972846 [GRCh37] Chr2:2q31.1	uncertain significance
NM_021192.3(HOXD11):c.418C>T (p.Leu140Phe)	single nucleotide variant	not specified [RCV004152373]	Chr2:176107773 [GRCh38] Chr2:176972501 [GRCh37] Chr2:2q31.1	uncertain significance
NM_021192.3(HOXD11):c.498C>A (p.Ser166Arg)	single nucleotide variant	not specified [RCV004074436]	Chr2:176107853 [GRCh38] Chr2:176972581 [GRCh37] Chr2:2q31.1	uncertain significance
NM_021192.3(HOXD11):c.150C>A (p.Asn50Lys)	single nucleotide variant	not specified [RCV004107765]	Chr2:176107505 [GRCh38] Chr2:176972233 [GRCh37] Chr2:2q31.1	uncertain significance
NM_021192.3(HOXD11):c.373A>T (p.Met125Leu)	single nucleotide variant	not specified [RCV004075647]	Chr2:176107728 [GRCh38] Chr2:176972456 [GRCh37] Chr2:2q31.1	uncertain significance
NM_021192.3(HOXD11):c.15C>G (p.Asp5Glu)	single nucleotide variant	not specified [RCV004138571]	Chr2:176107370 [GRCh38] Chr2:176972098 [GRCh37] Chr2:2q31.1	uncertain significance
NM_021192.3(HOXD11):c.232G>A (p.Gly78Ser)	single nucleotide variant	not specified [RCV004259165]	Chr2:176107587 [GRCh38] Chr2:176972315 [GRCh37] Chr2:2q31.1	uncertain significance
NM_021192.3(HOXD11):c.632G>T (p.Gly211Val)	single nucleotide variant	not specified [RCV004267765]	Chr2:176107987 [GRCh38] Chr2:176972715 [GRCh37] Chr2:2q31.1	uncertain significance
NM_021192.3(HOXD11):c.235G>C (p.Gly79Arg)	single nucleotide variant	not specified [RCV004260607]	Chr2:176107590 [GRCh38] Chr2:176972318 [GRCh37] Chr2:2q31.1	uncertain significance
NM_021192.3(HOXD11):c.342T>C (p.Ala114=)	single nucleotide variant	not provided [RCV003436258]	Chr2:176107697 [GRCh38] Chr2:176972425 [GRCh37] Chr2:2q31.1	likely benign
NM_021192.3(HOXD11):c.104T>C (p.Leu35Pro)	single nucleotide variant	not specified [RCV004402097]	Chr2:176107459 [GRCh38] Chr2:176972187 [GRCh37] Chr2:2q31.1	uncertain significance
NM_021192.3(HOXD11):c.458C>A (p.Pro153Gln)	single nucleotide variant	not specified [RCV004402101]	Chr2:176107813 [GRCh38] Chr2:176972541 [GRCh37] Chr2:2q31.1	uncertain significance
NM_021192.3(HOXD11):c.658G>A (p.Gly220Ser)	single nucleotide variant	not specified [RCV004402102]	Chr2:176108013 [GRCh38] Chr2:176972741 [GRCh37] Chr2:2q31.1	uncertain significance
NM_021192.3(HOXD11):c.7G>C (p.Asp3His)	single nucleotide variant	not specified [RCV004402104]	Chr2:176107362 [GRCh38] Chr2:176972090 [GRCh37] Chr2:2q31.1	uncertain significance
NM_021192.3(HOXD11):c.152T>G (p.Leu51Arg)	single nucleotide variant	not specified [RCV004402098]	Chr2:176107507 [GRCh38] Chr2:176972235 [GRCh37] Chr2:2q31.1	uncertain significance
NM_021192.3(HOXD11):c.305G>A (p.Gly102Asp)	single nucleotide variant	not specified [RCV004402099]	Chr2:176107660 [GRCh38] Chr2:176972388 [GRCh37] Chr2:2q31.1	uncertain significance
NM_021192.3(HOXD11):c.32C>A (p.Ala11Glu)	single nucleotide variant	not specified [RCV004402100]	Chr2:176107387 [GRCh38] Chr2:176972115 [GRCh37] Chr2:2q31.1	uncertain significance
NM_021192.3(HOXD11):c.719G>A (p.Gly240Asp)	single nucleotide variant	not specified [RCV004402103]	Chr2:176108074 [GRCh38] Chr2:176972802 [GRCh37] Chr2:2q31.1	uncertain significance
NM_021192.3(HOXD11):c.848G>T (p.Arg283Leu)	single nucleotide variant	not specified [RCV004402105]	Chr2:176108973 [GRCh38] Chr2:176973701 [GRCh37] Chr2:2q31.1	uncertain significance
NM_021192.3(HOXD11):c.888A>T (p.Arg296Ser)	single nucleotide variant	not specified [RCV004402106]	Chr2:176109013 [GRCh38] Chr2:176973741 [GRCh37] Chr2:2q31.1	uncertain significance

miRNA Target Status

Predicted Target Of

	Summary Value
Count of predictions:	613
Count of miRNA genes:	426
Interacting mature miRNAs:	455
Transcripts:	ENST00000249504, ENST00000498438
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

HOXD11_2590

Human Assembly	Chr	Position (strand)	Source	JBrowse
GRCh37	2	176,973,808 - 176,974,439	UniSTS	GRCh37
Build 36	2	176,682,054 - 176,682,685	RGD	NCBI36
Celera	2	170,582,953 - 170,583,584	RGD
HuRef	2	168,851,032 - 168,851,663	UniSTS

UniSTS:481748

Human Assembly	Chr	Position (strand)	Source	JBrowse
HuRef	2	168,849,568 - 168,851,144	UniSTS

UniSTS:482718

Human Assembly	Chr	Position (strand)	Source	JBrowse
HuRef	2	168,849,568 - 168,851,195	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

226

Low

696

297

221

274

542

109

215

Below cutoff

317

481

252

169

2698

711

728

551

208

730

1625

View RNA-SEQ Expression Data

Sequence

Nucleotide Sequences


RefSeq Transcripts	NG_008133	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	NM_021192	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XR_007073114	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XR_008486353	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	AC009336	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	AF154915	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	AK309681	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	BC109394	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	BE260674	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	CH471058	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	CP068276	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	KT583954	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

RefSeq Acc Id:

ENST00000249504 ⟹ ENSP00000249504

Type:

CODING

Position:

Human Assembly	Chr	Position (strand)	Source
GRCh38.p14 Ensembl	2	176,107,280 - 176,109,754 (+)	Ensembl

RefSeq Acc Id:

ENST00000498438

Type:

CODING

Position:

Human Assembly	Chr	Position (strand)	Source
GRCh38.p14 Ensembl	2	176,104,216 - 176,109,754 (+)	Ensembl

RefSeq Acc Id:

NM_021192 ⟹ NP_067015

RefSeq Status:

REVIEWED

Type:

CODING

Position:

Human Assembly	Chr	Position (strand)	Source
GRCh38	2	176,107,280 - 176,109,754 (+)	NCBI
GRCh37	2	176,971,721 - 176,976,563 (+)	NCBI
Build 36	2	176,680,330 - 176,682,562 (+)	NCBI Archive
HuRef	2	168,849,568 - 168,851,540 (+)	ENTREZGENE
CHM1_1	2	176,977,935 - 176,980,184 (+)	NCBI
T2T-CHM13v2.0	2	176,595,402 - 176,597,882 (+)	NCBI

Sequence:

show sequence

CTCTTGTGCAATCGATGGCTCAGGTTGGCTGCGCGGGGAGCGGCCAGAGGCTCGCTGGCGCGCA
CGCCGCGGAGTCATGAACGACTTTGACGAGTGCGGCCAGAGCGCAGCCAGCATGTACCTGCCGG
GCTGCGCCTACTATGTGGCCCCGTCTGACTTCGCTAGCAAGCCTTCGTTCCTTTCCCAACCGTC
GTCCTGCCAGATGACTTTCCCCTACTCTTCCAACCTGGCTCCGCACGTCCAGCCCGTGCGCGAA
GTGGCCTTCCGCGACTACGGCCTGGAGCGCGCCAAGTGGCCGTACCGCGGCGGCGGCGGCGGCG
GCAGCGCGGGGGGCGGCAGCAGCGGGGGCGGCCCCGGCGGGGGCGGCGGCGGCGCGGGGGGCTA
CGCTCCCTACTACGCGGCGGCGGCGGCGGCGGCTGCGGCGGCCGCGGCGGCCGAGGAGGCGGCC
ATGCAACGCGAGCTTCTCCCGCCCGCGGGCCGCCGGCCGGACGTGCTCTTCAAGGCGCCTGAGC
CGGTGTGCGCTGCGCCGGGGCCGCCGCACGGCCCCGCGGGCGCCGCCTCCAACTTCTACAGCGC
GGTGGGCCGCAATGGCATCTTGCCACAGGGCTTCGACCAGTTCTACGAGGCAGCGCCCGGGCCC
CCGTTCGCCGGGCCGCAGCCCCCGCCGCCACCCGCGCCGCCACAGCCCGAGGGCGCAGCCGACA
AGGGCGACCCCAGGACCGGGGCTGGTGGCGGCGGGGGCAGTCCCTGCACCAAGGCGACCCCTGG
CTCGGAGCCCAAGGGGGCAGCAGAAGGCAGCGGTGGCGACGGCGAGGGCCCCCCGGGAGAGGCG
GGGGCCGAGAAGAGCAGCAGCGCAGTTGCCCCCCAGCGGTCCCGGAAAAAGCGCTGTCCCTATA
CCAAGTACCAGATCCGCGAACTGGAACGCGAGTTTTTCTTTAACGTGTACATAAACAAAGAGAA
AAGACTTCAACTCTCTCGGATGCTCAACCTCACTGACCGGCAAGTCAAAATCTGGTTCCAGAAT
CGCAGGATGAAAGAAAAGAAACTGAACAGAGACCGTCTGCAGTATTTCACTGGAAACCCCTTAT
TTTGAGAGCTCCAGGAAGCGCCCTCACCCCAGCCCCACTCACCCACCCTCCTTCCCACCAGCCT
GCTCTCCGCAGGCCCACTGTCCTTGGGTTTAATGACGTCTCTTCTCTGTGGAACTTCACGATTC
CTTCCCACGGTCAACTCGGGACCTCCCAGCGACCACTGCAGCCTGCGGACGAGGCCGGGACTTG
GCCGAGCGGATCCTAATAAGGGGAAAATGGTAAATGCAAACGTCCCGTTACAATTTTACCGCCA
GTGTGCTGTCGTTCCCCCTCCCCCTCTCCGAGTCCTCGTGGGGACACGGCGGGGTCTGTAGGAA
GTTGGGCCGGGTTGGGGGTTGCTAGAAGGCGCTGGTGTTTTGCTCTGAGTTTTAAGAGATCCCT
TCCTTCCTCTTCGGTGAATGCAGGTTATTTAAACTTTGGGAAATGTACTTTTAGTCTGTCATAT
CAAGGCATGAGTCACTGTCTTTTTTTGTGTGAATAAATGGTTTCTAGTAAAATGGAGGTTACAG
CTTCAATACACTGTATGAATTCTCCTCTTTGAGGTTTAGTGCCTCCTTAGGATATTTTAGTGGC
CAGAACCCATGCAACTGAAAATCGAATGAAATACTTTTTAG

hide sequence

RefSeq Acc Id:

XR_007073114

Type:

NON-CODING

Position:

Human Assembly	Chr	Position (strand)	Source
GRCh38	2	176,107,280 - 176,115,679 (+)	NCBI

RefSeq Acc Id:

XR_008486353

Type:

NON-CODING

Position:

Human Assembly	Chr	Position (strand)	Source
T2T-CHM13v2.0	2	176,595,402 - 176,599,952 (+)	NCBI

Protein Sequences


Protein RefSeqs	NP_067015	(Get FASTA)	NCBI Sequence Viewer
GenBank Protein	AAF79045	(Get FASTA)	NCBI Sequence Viewer
	AAI09395	(Get FASTA)	NCBI Sequence Viewer
	EAX11092	(Get FASTA)	NCBI Sequence Viewer
Ensembl Protein	ENSP00000249504
	ENSP00000249504.5
GenBank Protein	P31277	(Get FASTA)	NCBI Sequence Viewer

RefSeq Acc Id:

NP_067015 ⟸ NM_021192

- UniProtKB:

A6NIS4 (UniProtKB/Swiss-Prot), Q9NS02 (UniProtKB/Swiss-Prot), P31277 (UniProtKB/Swiss-Prot)

- Sequence:

show sequence

MNDFDECGQSAASMYLPGCAYYVAPSDFASKPSFLSQPSSCQMTFPYSSNLAPHVQPVREVAFR
DYGLERAKWPYRGGGGGGSAGGGSSGGGPGGGGGGAGGYAPYYAAAAAAAAAAAAAEEAAMQRE
LLPPAGRRPDVLFKAPEPVCAAPGPPHGPAGAASNFYSAVGRNGILPQGFDQFYEAAPGPPFAG
PQPPPPPAPPQPEGAADKGDPRTGAGGGGGSPCTKATPGSEPKGAAEGSGGDGEGPPGEAGAEK
SSSAVAPQRSRKKRCPYTKYQIRELEREFFFNVYINKEKRLQLSRMLNLTDRQVKIWFQNRRMK
EKKLNRDRLQYFTGNPLF

hide sequence

RefSeq Acc Id:

ENSP00000249504 ⟸ ENST00000249504

Protein Domains

Homeobox

Protein Structures

Name	Modeler	Protein Id	AA Range	Protein Structure
AF-P31277-F1-model_v2	AlphaFold	P31277	1-338	view protein structure

Promoters

RGD ID:

6797596

Promoter ID:

HG_KWN:36038

Type:

CpG-Island

SO ACC ID:

SO:0000170

Source:

MPROMDB

Tissues & Cell Lines:

HeLa_S3

Transcripts:

ENST00000354571, ENST00000392538, OTTHUMT00000255691

Position:

Human Assembly	Chr	Position (strand)	Source
Build 36	2	176,680,096 - 176,680,596 (+)	MPROMDB

Additional Information

External Database Links

Database	Acc Id	Source(s)
AGR Gene	HGNC:5134	AgrOrtholog
COSMIC	HOXD11	COSMIC
Ensembl Genes	ENSG00000128713	Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript	ENST00000249504	ENTREZGENE
	ENST00000249504.7	UniProtKB/Swiss-Prot
Gene3D-CATH	Homeodomain-like	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
GTEx	ENSG00000128713	GTEx
HGNC ID	HGNC:5134	ENTREZGENE
Human Proteome Map	HOXD11	Human Proteome Map
InterPro	DUF3528	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	Homeobox-like_sf	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	Homeobox_CS	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	Homeobox_dom	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	Homeobox_metazoa	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report	hsa:3237	UniProtKB/Swiss-Prot
NCBI Gene	3237	ENTREZGENE
OMIM	142986	OMIM
PANTHER	HOMEOBOX PROTEIN HOX-A11-RELATED	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	HOMEOBOX PROTEIN HOX-D11	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam	DUF3528	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	Homeodomain	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PharmGKB	PA29408	PharmGKB
PRINTS	HOMEOBOX	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PROSITE	HOMEOBOX_1	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	HOMEOBOX_2	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART	HOX	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP	SSF46689	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt	A6NIS4	ENTREZGENE
	HXD11_HUMAN	UniProtKB/Swiss-Prot, ENTREZGENE
	Q14DW8_HUMAN	UniProtKB/TrEMBL
	Q9NS02	ENTREZGENE
UniProt Secondary	A6NIS4	UniProtKB/Swiss-Prot
	Q9NS02	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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