Hoxd1 (homeobox D1) - Rat Genome Database

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Gene: Hoxd1 (homeobox D1) Mus musculus
Analyze
Symbol: Hoxd1
Name: homeobox D1
RGD ID: 1319376
MGI Page MGI
Description: Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Acts upstream of or within embryonic skeletal system development; neuron differentiation; and sensory perception of pain. Located in nucleus. Is expressed in several structures, including early embryo; embryo mesenchyme; genitourinary system; intestine epithelium; and nervous system. Orthologous to human HOXD1 (homeobox D1).
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: homeo box D1; homeobox protein Hox-4.9; homeobox protein Hox-D1; Hox-4.; Hox-4.9
RGD Orthologs
Human
Rat
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCm39 - Mouse Genome Assembly GRCm39
Position:
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39274,593,324 - 74,595,486 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl274,593,324 - 74,595,486 (+)EnsemblGRCm39 Ensembl
GRCm38274,762,980 - 74,765,142 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl274,762,980 - 74,765,142 (+)EnsemblGRCm38mm10GRCm38
MGSCv37274,601,037 - 74,603,199 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36274,563,819 - 74,565,982 (+)NCBIMGSCv36mm8
Celera276,433,115 - 76,435,276 (+)NCBICelera
Cytogenetic Map2C3NCBI
cM Map244.13NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component
nucleoplasm  (ISO,TAS)
nucleus  (IBA,IDA)

Phenotype Annotations     Click to see Annotation Detail View
References

References - curated
# Reference Title Reference Citation
1. Mouse brain organization revealed through direct genome-scale TF expression analysis. Gray PA, etal., Science 2004 Dec 24;306(5705):2255-7.
2. MGDs mouse GO annotations MGD data from the GO Consortium
3. MGD IEA MGD IEA
4. Mouse MP Annotation Import Pipeline RGD automated import pipeline
5. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:1348361   PMID:1356009   PMID:1358459   PMID:1680771   PMID:1682814   PMID:1688181   PMID:1720547   PMID:2906120   PMID:7915637   PMID:7956823   PMID:8102800   PMID:8889548  
PMID:8978061   PMID:9342041   PMID:10536059   PMID:11209945   PMID:11455954   PMID:11511348   PMID:11544178   PMID:11731253   PMID:12477932   PMID:15042701   PMID:15192229   PMID:15253936  
PMID:15995706   PMID:16602821   PMID:16971476   PMID:17467687   PMID:17554625   PMID:17698011   PMID:17942481   PMID:18252796   PMID:18498732   PMID:18498735   PMID:19204410   PMID:20059953  
PMID:20211142   PMID:21151121   PMID:21267068   PMID:21567651   PMID:21873635   PMID:22701719   PMID:22872084   PMID:24075990   PMID:24378336   PMID:28009287   PMID:28041967   PMID:28188179  
PMID:29031500   PMID:32479258   PMID:33257809   PMID:34711654   PMID:35514355   PMID:35770682  


Genomics

Comparative Map Data
Hoxd1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39274,593,324 - 74,595,486 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl274,593,324 - 74,595,486 (+)EnsemblGRCm39 Ensembl
GRCm38274,762,980 - 74,765,142 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl274,762,980 - 74,765,142 (+)EnsemblGRCm38mm10GRCm38
MGSCv37274,601,037 - 74,603,199 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36274,563,819 - 74,565,982 (+)NCBIMGSCv36mm8
Celera276,433,115 - 76,435,276 (+)NCBICelera
Cytogenetic Map2C3NCBI
cM Map244.13NCBI
HOXD1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh382176,188,668 - 176,190,907 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl2176,188,668 - 176,190,907 (+)EnsemblGRCh38hg38GRCh38
GRCh372177,053,396 - 177,055,635 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 362176,761,553 - 176,763,881 (+)NCBINCBI36Build 36hg18NCBI36
Build 342176,878,813 - 176,881,142NCBI
Celera2170,662,486 - 170,664,814 (+)NCBICelera
Cytogenetic Map2q31.1NCBI
HuRef2168,930,260 - 168,932,588 (+)NCBIHuRef
CHM1_12177,059,181 - 177,061,509 (+)NCBICHM1_1
T2T-CHM13v2.02176,676,799 - 176,679,038 (+)NCBIT2T-CHM13v2.0
Hoxd1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8380,073,041 - 80,075,180 (+)NCBIGRCr8
mRatBN7.2359,665,629 - 59,667,769 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl359,665,629 - 59,667,769 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx363,052,804 - 63,054,943 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0371,636,445 - 71,638,584 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0369,401,510 - 69,403,649 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0361,685,619 - 61,687,758 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl361,685,619 - 61,687,758 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0368,151,156 - 68,153,295 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4357,377,839 - 57,379,978 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1357,274,308 - 57,275,611 (+)NCBI
Celera359,186,877 - 59,189,016 (+)NCBICelera
Cytogenetic Map3q23NCBI
Hoxd1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495540320,476,645 - 20,478,604 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495540320,476,813 - 20,478,604 (-)NCBIChiLan1.0ChiLan1.0
HOXD1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v21378,856,146 - 78,858,397 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan12B78,871,121 - 78,873,372 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v02B63,468,317 - 63,470,658 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.12B181,176,789 - 181,179,105 (+)NCBIpanpan1.1PanPan1.1panPan2
HOXD1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.13619,995,326 - 19,997,059 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl3619,995,323 - 19,997,072 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha3620,004,663 - 20,006,594 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.03620,136,108 - 20,138,025 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl3620,136,051 - 20,138,025 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.13620,210,053 - 20,211,984 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.03620,210,733 - 20,212,644 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.03620,322,637 - 20,324,574 (+)NCBIUU_Cfam_GSD_1.0
Hoxd1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024405303137,119,139 - 137,121,389 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049365095,673,184 - 5,674,521 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049365095,673,184 - 5,674,636 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
HOXD1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1581,987,769 - 81,990,134 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11581,987,618 - 81,990,026 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21591,455,233 - 91,457,417 (+)NCBISscrofa10.2Sscrofa10.2susScr3
HOXD1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11061,764,519 - 61,766,846 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl1061,764,741 - 61,766,081 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_023666040137,843,997 - 137,846,232 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Hoxd1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462478713,325,276 - 13,326,824 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462478713,325,232 - 13,327,400 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:165
Count of miRNA genes:154
Interacting mature miRNAs:155
Transcripts:ENSMUST00000047793
Prediction methods:Miranda, Rnahybrid
Result types:miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.


QTLs in Region (GRCm39)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
13464141Hbbcq3_mhemoglobin concentration QTL 3 (mouse)25244801986448136Mouse
13824983Vclq1_mcurvilinear velocity QTL 1 (mouse)261830344136841920Mouse
1301402Ap2q_malcohol preference 2 QTL (mouse)Not determined24352061277520756Mouse
1300761Lgth1_mbody length 1 (mouse)Not determined25170327685703425Mouse
4141236Hbnr5_mHeligmosomoides bakeri nematode resistance 5 (mouse)Not determined31214567105143570Mouse
1302174Dssc2_mdextran sodium sulfate induced colitis QTL2 (mouse)Not determined224224632148700377Mouse
1301405Etohr_methanol response acute (mouse)Not determined26300595497006113Mouse
1301660Iba1_minduction of brown adipocytes 1 (mouse)Not determined267647887101648142Mouse
1558915W3q1_mweight 3 weeks QTL 1 (mouse)Not determined220897778118894840Mouse
1300875Taste1_mtaste-saccharin preference 1 (mouse)Not determined25092317584923278Mouse
1301769Orgwq2_morgan weight QTL 2 (mouse)Not determined2388712693421651Mouse
1357454Kidq1_mkidney weight QTL 1 (mouse)Not determined220897778118894840Mouse
1357577Trmq3_mT cell ratio modifier QTL 3 (mouse)Not determined260520612119355518Mouse
1558966W10q9_mweight 10 weeks QTL 9 (mouse)Not determined220897778118894840Mouse
4141854T2dm2sa_mtype 2 diabetes mellitus 2 in SMXA RI mice (mouse)Not determined229307947148374934Mouse
1300662Etohila_methanol induced locomotor activity (mouse)Not determined26300595497006113Mouse
1300788Cia2_mcollagen induced arthritis QTL 2 (mouse)Not determined24352061277520756Mouse
10053681Lith24_mlithogenic gene 24 (mouse)Not determined26300595497006113Mouse
1301048Actre2_mactivity response to ethanol 2 (mouse)Not determined26300595497006113Mouse
1300671Cia4_mcollagen induced arthritis QTL 4 (mouse)Not determined24352061277520756Mouse
1357881Estoq1_membryo survival total QTL 1 (mouse)Not determined220897778118894840Mouse
5491197Mobq5_mmultigenic obesity QTL 5 (mouse)Not determined265269746162518926Mouse
1301948Elsgp3_melevated serum gp70 3 (mouse)Not determined268724269102724407Mouse
1301411Pitm1_mprion incubation time 1 (mouse)Not determined24352061277520756Mouse
4141069Pbwg1.5_mpostnatal body weight growth 1.5 (mouse)Not determined4352061277520756Mouse
1558820Moo1_mmodifier of Odc1 (mouse)Not determined174826974682269934Mouse
4142088Parms1_mpatched associated RMS 1 (mouse)Not determined74524117114123532Mouse
12738429Lfibq18_mliver fibrosis QTL 18 (mouse)25791999191919991Mouse
39128209Lwq14_mliver weight QTL 14 (mouse)220897778118894840Mouse
1558738W6q1_mweight 6 weeks QTL 1 (mouse)Not determined220897778118894840Mouse
11528549Sluc31_msusceptibility to lung cancer 31 (mouse)274524117129213005Mouse
1300568Hdl1_mhigh density lipoprotein (HDL) level 1 (mouse)Not determined24826974682269934Mouse
1301059Hrtfm1_mheart failure modifier 1 (mouse)Not determined26759194074964933Mouse
1301703Bomd3_mbone mineral density 3 (mouse)Not determined26300595497006113Mouse
1301747Eae21_mexperimental allergic encephalomyelitis 21 (mouse)Not determined24826974682269934Mouse
1301235Alcw4_malcohol withdrawal 4 (mouse)Not determined24826974682269934Mouse
4141406Alpq2_malcohol preference QTL 2 (mouse)Not determined25752411791524288Mouse
10755526Lymph1_mlymphocyte differential 1 (mouse)25081931484819314Mouse
13463471Hctq6_mhematocrit QTL 6 (mouse)25244801986448136Mouse
1301873Hsl1_mhyperoxia susceptibility locus 1 (mouse)Not determined26357015497570301Mouse
1558899Egq1_mearly growth QTL 1 (mouse)Not determined220897778118894840Mouse
1357681Hrtq1_mheart weight QTL 1 (mouse)Not determined220897778118894840Mouse
1301109Dntcs2_mdental caries susceptibility 2 (mouse)Not determined240885493114910165Mouse
1357436Splq1_mspleen weight QTL 1 (mouse)Not determined220897778118894840Mouse
10755532Lymph5_mlymphocyte differential 5 (mouse)24419901778199017Mouse
1301882Etohc2_methanol consumption 2 (mouse)Not determined268724269102724407Mouse
11532740Pbwg1.10_mpostnatal body weight growth 1.10 (mouse)24813241282132495Mouse
1300577Capsq1_mcapsaicin sensitivity related QTL 1 (mouse)Not determined22760206084013384Mouse
1301344Lith1_mlithogenic gene 1 (mouse)Not determined245347635145312647Mouse
13463482Mchq17_mmean corpuscular hemoglobin QTL 17 (mouse)267647887101648142Mouse
1301480Pbwg1_mpostnatal body weight growth 1 (mouse)Not determined24182071975820843Mouse
10044002Hdl7_mHDL level 7 (mouse)Not determined26300595497006113Mouse

Markers in Region
X60034  
Mouse AssemblyChrPosition (strand)SourceJBrowse
GRCm38274,764,437 - 74,764,631UniSTSGRCm38
MGSCv37274,602,494 - 74,602,688UniSTSGRCm37
Celera276,434,571 - 76,434,765UniSTS
Cytogenetic Map2C3UniSTS
cM Map245.0UniSTS
Whitehead/MRC_RH21172.31UniSTS
Whitehead_YAC2 UniSTS
D2Tfv13  
Mouse AssemblyChrPosition (strand)SourceJBrowse
Cytogenetic Map2C3UniSTS
cM Map245.0UniSTS
cM Map2 UniSTS
D2Tfv14  
Mouse AssemblyChrPosition (strand)SourceJBrowse
GRCm38274,764,670 - 74,764,895UniSTSGRCm38
MGSCv37274,602,727 - 74,602,952UniSTSGRCm37
Celera276,434,804 - 76,435,029UniSTS
Cytogenetic Map2C3UniSTS
cM Map245.0UniSTS
cM Map2 UniSTS
Hoxd1  
Mouse AssemblyChrPosition (strand)SourceJBrowse
Cytogenetic Map2C3UniSTS
cM Map245.0UniSTS
X60034  
Mouse AssemblyChrPosition (strand)SourceJBrowse
GRCm38274,764,398 - 74,764,481UniSTSGRCm38
MGSCv37274,602,455 - 74,602,538UniSTSGRCm37
Celera276,434,532 - 76,434,615UniSTS
Cytogenetic Map2C3UniSTS
Whitehead/MRC_RH21172.31UniSTS


Expression

RNA-SEQ Expression


Sequence


Ensembl Acc Id: ENSMUST00000047793   ⟹   ENSMUSP00000043078
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl274,593,324 - 74,595,486 (+)Ensembl
GRCm38.p6 Ensembl274,762,980 - 74,765,142 (+)Ensembl
RefSeq Acc Id: NM_010467   ⟹   NP_034597
RefSeq Status: VALIDATED
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39274,593,324 - 74,595,486 (+)NCBI
GRCm38274,762,980 - 74,765,142 (+)ENTREZGENE
MGSCv37274,601,037 - 74,603,199 (+)RGD
Celera276,433,115 - 76,435,276 (+)RGD
cM Map2 ENTREZGENE
Sequence:
Protein Sequences
Protein RefSeqs NP_034597 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAA37853 (Get FASTA)   NCBI Sequence Viewer  
  AAI20538 (Get FASTA)   NCBI Sequence Viewer  
  AAI20540 (Get FASTA)   NCBI Sequence Viewer  
  CAA42637 (Get FASTA)   NCBI Sequence Viewer  
  EDL27181 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSMUSP00000043078
  ENSMUSP00000043078.4
GenBank Protein Q01822 (Get FASTA)   NCBI Sequence Viewer  
RefSeq Acc Id: NP_034597   ⟸   NM_010467
- UniProtKB: Q0VBQ9 (UniProtKB/Swiss-Prot),   Q01822 (UniProtKB/Swiss-Prot)
- Sequence:
Ensembl Acc Id: ENSMUSP00000043078   ⟸   ENSMUST00000047793

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q01822-F1-model_v2 AlphaFold Q01822 1-328 view protein structure

Promoters
RGD ID:6832396
Promoter ID:MM_KWN:29770
Type:CpG-Island
SO ACC ID:SO:0000170
Source:MPROMDB
Tissues & Cell Lines:Kidney
Transcripts:OTTMUST00000040109,   OTTMUST00000040130
Position:
Mouse AssemblyChrPosition (strand)Source
MGSCv36274,600,901 - 74,601,401 (-)MPROMDB
RGD ID:6877682
Promoter ID:EPDNEW_M2291
Type:multiple initiation site
Name:Hoxd1_1
Description:Mus musculus homeobox D1 , mRNA.
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm38274,763,004 - 74,763,064EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene MGI:96201 AgrOrtholog
Ensembl Genes ENSMUSG00000042448 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSMUST00000047793 ENTREZGENE
  ENSMUST00000047793.6 UniProtKB/Swiss-Prot
Gene3D-CATH Homeodomain-like UniProtKB/Swiss-Prot
InterPro Homeobox-like_sf UniProtKB/Swiss-Prot
  Homeobox_CS UniProtKB/Swiss-Prot
  Homeobox_dom UniProtKB/Swiss-Prot
  Homeobox_metazoa UniProtKB/Swiss-Prot
  HXA1/B1/D1 UniProtKB/Swiss-Prot
KEGG Report mmu:15429 UniProtKB/Swiss-Prot
MGD MGI:96201 ENTREZGENE
NCBI Gene 15429 ENTREZGENE
PANTHER HOMEOBOX PROTEIN HOX-D1 UniProtKB/Swiss-Prot
  PTHR45946 UniProtKB/Swiss-Prot
Pfam Homeodomain UniProtKB/Swiss-Prot
PhenoGen Hoxd1 PhenoGen
PRINTS HOMEOBOX UniProtKB/Swiss-Prot
PROSITE HOMEOBOX_1 UniProtKB/Swiss-Prot
  HOMEOBOX_2 UniProtKB/Swiss-Prot
SMART HOX UniProtKB/Swiss-Prot
Superfamily-SCOP SSF46689 UniProtKB/Swiss-Prot
UniProt HXD1_MOUSE UniProtKB/Swiss-Prot, ENTREZGENE
  Q0VBQ9 ENTREZGENE
UniProt Secondary Q0VBQ9 UniProtKB/Swiss-Prot