HOXD11 (homeobox D11) - Rat Genome Database

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Gene: HOXD11 (homeobox D11) Homo sapiens
Analyze
Symbol: HOXD11
Name: homeobox D11
RGD ID: 1346896
HGNC Page HGNC
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 cell differentiation; and regionalization. Located in nucleoplasm.
Type: protein-coding
RefSeq Status: REVIEWED
Also 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
Mouse
Rat
Chinchilla
Bonobo
Dog
Pig
Green Monkey
Alliance Genes
More Info more info ...
Allele / Splice: See ClinVar data
Latest Assembly: GRCh38 - Human Genome Assembly GRCh38
Position:
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl2176,104,216 - 176,109,754 (+)EnsemblGRCh38hg38GRCh38
GRCh382176,107,280 - 176,109,754 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh372176,972,008 - 176,974,482 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 362176,680,330 - 176,682,562 (+)NCBINCBI36hg18NCBI36
Build 342176,797,590 - 176,799,823NCBI
Celera2170,581,234 - 170,583,461 (+)NCBI
Cytogenetic Map2q31.1NCBI
HuRef2168,849,568 - 168,851,540 (+)NCBIHuRef
CHM1_12176,977,935 - 176,980,184 (+)NCBICHM1_1
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
References

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  


Genomics

Comparative Map Data
HOXD11
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl2176,104,216 - 176,109,754 (+)EnsemblGRCh38hg38GRCh38
GRCh382176,107,280 - 176,109,754 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh372176,972,008 - 176,974,482 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 362176,680,330 - 176,682,562 (+)NCBINCBI36hg18NCBI36
Build 342176,797,590 - 176,799,823NCBI
Celera2170,581,234 - 170,583,461 (+)NCBI
Cytogenetic Map2q31.1NCBI
HuRef2168,849,568 - 168,851,540 (+)NCBIHuRef
CHM1_12176,977,935 - 176,980,184 (+)NCBICHM1_1
Hoxd11
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39274,509,902 - 74,517,360 (+)NCBIGRCm39mm39
GRCm39 Ensembl274,509,901 - 74,517,360 (+)Ensembl
GRCm38274,679,558 - 74,687,016 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl274,679,557 - 74,687,016 (+)EnsemblGRCm38mm10GRCm38
MGSCv37274,520,450 - 74,522,195 (+)NCBIGRCm37mm9NCBIm37
MGSCv36274,483,232 - 74,484,977 (+)NCBImm8
Celera276,352,501 - 76,354,246 (+)NCBICelera
Cytogenetic Map2C3NCBI
cM Map244.13NCBI
Hoxd11
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2359,584,840 - 59,587,257 (+)NCBImRatBN7.2
Rnor_6.0361,604,256 - 61,606,874 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl361,604,672 - 61,606,400 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0368,071,282 - 68,076,686 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Celera359,104,507 - 59,109,071 (+)NCBICelera
Cytogenetic Map3q23NCBI
Hoxd11
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0NW_00495540320,541,870 - 20,556,574 (-)NCBIChiLan1.0ChiLan1.0
HOXD11
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.12B181,095,347 - 181,098,680 (+)NCBIpanpan1.1PanPan1.1panPan2
Mhudiblu_PPA_v02B63,386,806 - 63,398,777 (+)NCBIMhudiblu_PPA_v0panPan3
HOXD11
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.13619,913,064 - 19,926,868 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl3619,914,431 - 19,916,766 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha3619,921,364 - 19,929,032 (+)NCBI
ROS_Cfam_1.03620,052,553 - 20,060,228 (+)NCBI
UMICH_Zoey_3.13620,129,998 - 20,134,442 (+)NCBI
UNSW_CanFamBas_1.03620,130,689 - 20,135,144 (+)NCBI
UU_Cfam_GSD_1.03620,239,278 - 20,246,796 (+)NCBI
HOXD11
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1581,908,460 - 81,910,281 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11581,906,654 - 81,910,765 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21591,374,469 - 91,377,543 (+)NCBISscrofa10.2Sscrofa10.2susScr3
HOXD11
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11061,681,474 - 61,693,974 (+)NCBI
ChlSab1.1 Ensembl1061,682,400 - 61,684,168 (+)Ensembl
Vero_WHO_p1.0NW_023666040137,925,780 - 137,928,157 (-)NCBI

Position Markers
HOXD11_2590  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh372176,973,808 - 176,974,439UniSTSGRCh37
Build 362176,682,054 - 176,682,685RGDNCBI36
Celera2170,582,953 - 170,583,584RGD
HuRef2168,851,032 - 168,851,663UniSTS
UniSTS:481748  
Human AssemblyChrPosition (strand)SourceJBrowse
HuRef2168,849,568 - 168,851,144UniSTS
UniSTS:482718  
Human AssemblyChrPosition (strand)SourceJBrowse
HuRef2168,849,568 - 168,851,195UniSTS

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.


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 76 4 2 2 2 10 23 36 38 226 57 2
Low 696 13 8 7 9 297 17 221 274 542 109 5 70 215 1
Below cutoff 317 481 252 66 169 38 2698 711 728 87 551 208 29 730 1625 1

Sequence


Reference Sequences
RefSeq Acc Id: ENST00000249504   ⟹   ENSP00000249504
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl2176,107,280 - 176,109,754 (+)Ensembl
RefSeq Acc Id: ENST00000498438
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl2176,104,216 - 176,109,754 (+)Ensembl
RefSeq Acc Id: NM_021192   ⟹   NP_067015
RefSeq Status: REVIEWED
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh382176,107,280 - 176,109,754 (+)NCBI
GRCh372176,971,721 - 176,976,563 (+)NCBI
Build 362176,680,330 - 176,682,562 (+)NCBI Archive
HuRef2168,849,568 - 168,851,540 (+)ENTREZGENE
CHM1_12176,977,935 - 176,980,184 (+)NCBI
Sequence:
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  
  P31277 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_067015   ⟸   NM_021192
- UniProtKB: P31277 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSP00000249504   ⟸   ENST00000249504
Protein Domains
Homeobox

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 AssemblyChrPosition (strand)Source
Build 362176,680,096 - 176,680,596 (+)MPROMDB

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 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

Additional Information

Database Acc Id Source(s)
AGR Gene HGNC:5134 AgrOrtholog
COSMIC HOXD11 COSMIC
Ensembl Genes ENSG00000128713 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Protein ENSP00000249504 ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENST00000249504 ENTREZGENE, UniProtKB/Swiss-Prot
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
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 HXD11_HUMAN UniProtKB/Swiss-Prot, ENTREZGENE
  Q14DW8_HUMAN UniProtKB/TrEMBL
UniProt Secondary A6NIS4 UniProtKB/Swiss-Prot
  Q9NS02 UniProtKB/Swiss-Prot