HOXD1 (homeobox D1) - Rat Genome Database

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Gene: HOXD1 (homeobox D1) Homo sapiens
Analyze
Symbol: HOXD1
Name: homeobox D1
RGD ID: 1319375
HGNC Page HGNC:5132
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 embryonic skeletal system development; neuron differentiation; and sensory perception of pain. Located in nucleoplasm.
Type: protein-coding
RefSeq Status: REVIEWED
Previously known as: homeo box 4G; homeo box D1; homeobox protein Hox-D1; homeobox protein Hox-GG; Hox-4.7; HOX4; HOX4G
RGD Orthologs
Mouse
Rat
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Allele / Splice: See ClinVar data
Latest Assembly: GRCh38 - Human Genome Assembly GRCh38
Position:
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
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
chromatin  (ISA)
nucleoplasm  (IDA)
nucleus  (IBA,IEA)

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:2576652   PMID:7501971   PMID:7913891   PMID:8104620   PMID:10364522   PMID:10908280   PMID:11060466   PMID:11455954   PMID:11731253   PMID:11857506  
PMID:12477932   PMID:19274049   PMID:19453261   PMID:19490893   PMID:19938081   PMID:20211142   PMID:20852632   PMID:21501586   PMID:21873635   PMID:22930747   PMID:23535375   PMID:28473536  
PMID:33559901   PMID:33961781   PMID:37655555   PMID:37827698   PMID:39450540  


Genomics

Comparative Map Data
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
(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
(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

Variants

.
Variants in HOXD1
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 2q31.1-31.2(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 2q31.1-31.2(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(chr2:176951487-177070756)x3 copy number gain not provided [RCV000740717] Chr2:176951487..177070756 [GRCh37]
Chr2:2q31.1		 benign
NM_024501.3(HOXD1):c.191C>T (p.Ser64Leu) single nucleotide variant not specified [RCV004295907] Chr2:176188992 [GRCh38]
Chr2:177053720 [GRCh37]
Chr2:2q31.1		 uncertain significance
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 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 2q31.1-31.2(chr2:176310551-179092634)x1 copy number loss not provided [RCV000849015] Chr2:176310551..179092634 [GRCh37]
Chr2:2q31.1-31.2		 pathogenic
GRCh37/hg19 2q31.1-32.1(chr2:173538954-186401606)x1 copy number loss not provided [RCV000846537] Chr2:173538954..186401606 [GRCh37]
Chr2:2q31.1-32.1		 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 2q24.2-34(chr2:163233162-211927188)x3 copy number gain not provided [RCV001005349] Chr2:163233162..211927188 [GRCh37]
Chr2:2q24.2-34		 pathogenic
NM_024501.3(HOXD1):c.308dup (p.Ala104fs) duplication not provided [RCV001090466] Chr2:176189104..176189105 [GRCh38]
Chr2:177053832..177053833 [GRCh37]
Chr2:2q31.1		 uncertain significance
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 2q24.2-31.3(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 osseus syndactyly [RCV001352646] Chr2:171999572..182774361 [GRCh37]
Chr2:2q31.1-31.3		 pathogenic
GRCh37/hg19 2q31.1-35(chr2:169829974-215521436) copy number gain not specified [RCV002053265] Chr2:169829974..215521436 [GRCh37]
Chr2:2q31.1-35		 pathogenic
GRCh37/hg19 2q31.1(chr2:174673094-177275625)x3 copy number gain not provided [RCV001825257] Chr2:174673094..177275625 [GRCh37]
Chr2:2q31.1		 not provided
Single allele deletion Split hand-foot malformation 5 [RCV002264898] Chr2:171524396..178694337 [GRCh37]
Chr2:2q31.1-31.2		 pathogenic
NM_024501.3(HOXD1):c.472G>C (p.Gly158Arg) single nucleotide variant not specified [RCV004308996] Chr2:176189273 [GRCh38]
Chr2:177054001 [GRCh37]
Chr2:2q31.1		 uncertain significance
NM_024501.3(HOXD1):c.335G>T (p.Gly112Val) single nucleotide variant not specified [RCV004325068] Chr2:176189136 [GRCh38]
Chr2:177053864 [GRCh37]
Chr2:2q31.1		 uncertain significance
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_024501.3(HOXD1):c.262G>A (p.Glu88Lys) single nucleotide variant not specified [RCV004137146] Chr2:176189063 [GRCh38]
Chr2:177053791 [GRCh37]
Chr2:2q31.1		 uncertain significance
NM_024501.3(HOXD1):c.931C>A (p.Pro311Thr) single nucleotide variant not specified [RCV004129905] Chr2:176190086 [GRCh38]
Chr2:177054814 [GRCh37]
Chr2:2q31.1		 uncertain significance
NM_024501.3(HOXD1):c.951C>A (p.Asn317Lys) single nucleotide variant not specified [RCV004123897] Chr2:176190106 [GRCh38]
Chr2:177054834 [GRCh37]
Chr2:2q31.1		 uncertain significance
NM_024501.3(HOXD1):c.452A>G (p.Gln151Arg) single nucleotide variant not specified [RCV004208627] Chr2:176189253 [GRCh38]
Chr2:177053981 [GRCh37]
Chr2:2q31.1		 uncertain significance
NM_024501.3(HOXD1):c.351C>G (p.Phe117Leu) single nucleotide variant not specified [RCV004229753] Chr2:176189152 [GRCh38]
Chr2:177053880 [GRCh37]
Chr2:2q31.1		 uncertain significance
NM_024501.3(HOXD1):c.802C>G (p.Leu268Val) single nucleotide variant not specified [RCV004208139] Chr2:176189957 [GRCh38]
Chr2:177054685 [GRCh37]
Chr2:2q31.1		 uncertain significance
NM_024501.3(HOXD1):c.799C>T (p.His267Tyr) single nucleotide variant not specified [RCV004185009] Chr2:176189954 [GRCh38]
Chr2:177054682 [GRCh37]
Chr2:2q31.1		 uncertain significance
NM_024501.3(HOXD1):c.752A>G (p.Asn251Ser) single nucleotide variant not specified [RCV004213736] Chr2:176189907 [GRCh38]
Chr2:177054635 [GRCh37]
Chr2:2q31.1		 uncertain significance
NM_024501.3(HOXD1):c.347A>G (p.Asp116Gly) single nucleotide variant not specified [RCV004148052] Chr2:176189148 [GRCh38]
Chr2:177053876 [GRCh37]
Chr2:2q31.1		 uncertain significance
NM_024501.3(HOXD1):c.382G>A (p.Gly128Ser) single nucleotide variant not specified [RCV004100199] Chr2:176189183 [GRCh38]
Chr2:177053911 [GRCh37]
Chr2:2q31.1		 uncertain significance
NM_024501.3(HOXD1):c.458A>C (p.Asp153Ala) single nucleotide variant not specified [RCV004105490] Chr2:176189259 [GRCh38]
Chr2:177053987 [GRCh37]
Chr2:2q31.1		 uncertain significance
NM_024501.3(HOXD1):c.328G>T (p.Gly110Trp) single nucleotide variant not specified [RCV004282934] Chr2:176189129 [GRCh38]
Chr2:177053857 [GRCh37]
Chr2:2q31.1		 uncertain significance
NM_024501.3(HOXD1):c.442C>T (p.Leu148Phe) single nucleotide variant not specified [RCV004402090] Chr2:176189243 [GRCh38]
Chr2:177053971 [GRCh37]
Chr2:2q31.1		 uncertain significance
NM_024501.3(HOXD1):c.670G>T (p.Gly224Trp) single nucleotide variant not specified [RCV004402091] Chr2:176189825 [GRCh38]
Chr2:177054553 [GRCh37]
Chr2:2q31.1		 uncertain significance
NM_024501.3(HOXD1):c.756G>C (p.Lys252Asn) single nucleotide variant not specified [RCV004402092] Chr2:176189911 [GRCh38]
Chr2:177054639 [GRCh37]
Chr2:2q31.1		 uncertain significance
NM_024501.3(HOXD1):c.920C>T (p.Ser307Phe) single nucleotide variant not specified [RCV004402094] Chr2:176190075 [GRCh38]
Chr2:177054803 [GRCh37]
Chr2:2q31.1		 uncertain significance
NM_024501.3(HOXD1):c.287C>A (p.Ala96Glu) single nucleotide variant not specified [RCV004402089] Chr2:176189088 [GRCh38]
Chr2:177053816 [GRCh37]
Chr2:2q31.1		 uncertain significance
NM_024501.3(HOXD1):c.335G>A (p.Gly112Glu) single nucleotide variant not specified [RCV004633032] Chr2:176189136 [GRCh38]
Chr2:177053864 [GRCh37]
Chr2:2q31.1		 uncertain significance
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:368
Count of miRNA genes:325
Interacting mature miRNAs:339
Transcripts:ENST00000331462
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 (GRCh38)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
407346172GWAS995148_Hurate measurement QTL GWAS995148 (human)5e-10urate measurementblood uric acid level (CMO:0000501)2176190041176190042Human
407367739GWAS1016715_Hglomerular filtration rate QTL GWAS1016715 (human)1e-14glomerular filtration rateglomerular filtration rate (CMO:0000490)2176188698176188699Human
406895373GWAS544349_Hglucose-dependent insulinotropic peptide measurement, glucose tolerance test QTL GWAS544349 (human)2e-08glucose-dependent insulinotropic peptide measurement, glucose tolerance test2176189453176189454Human

Markers in Region
RH68884  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh372177,055,411 - 177,055,609UniSTSGRCh37
Build 362176,763,657 - 176,763,855RGDNCBI36
Celera2170,664,590 - 170,664,788RGD
Cytogenetic Map2q31.1UniSTS
Cytogenetic Map2q31.2UniSTS
HuRef2168,932,364 - 168,932,562UniSTS
GeneMap99-GB4 RH Map2577.44UniSTS
NCBI RH Map21374.7UniSTS
HOXD1_1231  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh372177,054,932 - 177,055,663UniSTSGRCh37
Build 362176,763,178 - 176,763,909RGDNCBI36
Celera2170,664,111 - 170,664,842RGD
HuRef2168,931,885 - 168,932,616UniSTS


Expression

RNA-SEQ Expression

adipose tissue
alimentary part of gastrointestinal system
appendage
circulatory system
ectoderm
endocrine system
endoderm
entire extraembryonic component
exocrine system
hemolymphoid system
hepatobiliary system
integumental system
mesenchyme
mesoderm
musculoskeletal system
nervous system
renal system
reproductive system
respiratory system
sensory system
1202 2317 2389 1534 4227 1071 1812 1 316 629 168 2096 4548 4359 35 3206 809 1488 1390 157

Sequence


Ensembl Acc Id: ENST00000331462   ⟹   ENSP00000328598
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl2176,188,668 - 176,190,907 (+)Ensembl
RefSeq Acc Id: NM_024501   ⟹   NP_078777
RefSeq Status: REVIEWED
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh382176,188,668 - 176,190,907 (+)NCBI
GRCh372177,053,307 - 177,055,635 (+)ENTREZGENE
Build 362176,761,553 - 176,763,881 (+)NCBI Archive
HuRef2168,930,260 - 168,932,588 (+)ENTREZGENE
CHM1_12177,059,181 - 177,061,509 (+)NCBI
T2T-CHM13v2.02176,676,799 - 176,679,038 (+)NCBI
Sequence:
RefSeq Acc Id: XM_047444086   ⟹   XP_047300042
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh382176,188,668 - 176,190,907 (+)NCBI
RefSeq Acc Id: XM_054341650   ⟹   XP_054197625
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
T2T-CHM13v2.02176,676,799 - 176,679,038 (+)NCBI
RefSeq Acc Id: NP_078777   ⟸   NM_024501
- UniProtKB: B2RAB4 (UniProtKB/Swiss-Prot),   Q9GZZ0 (UniProtKB/Swiss-Prot),   Q96CA4 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSP00000328598   ⟸   ENST00000331462
RefSeq Acc Id: XP_047300042   ⟸   XM_047444086
- Peptide Label: isoform X1
RefSeq Acc Id: XP_054197625   ⟸   XM_054341650
- Peptide Label: isoform X1
Protein Domains
Homeobox

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q9GZZ0-F1-model_v2 AlphaFold Q9GZZ0 1-328 view protein structure

Promoters
RGD ID:6862138
Promoter ID:EPDNEW_H4234
Type:initiation region
Name:HOXD1_1
Description:homeobox D1
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Human AssemblyChrPosition (strand)Source
GRCh382176,188,668 - 176,188,728EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene HGNC:5132 AgrOrtholog
COSMIC HOXD1 COSMIC
Ensembl Genes ENSG00000128645 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENST00000331462 ENTREZGENE
  ENST00000331462.6 UniProtKB/Swiss-Prot
Gene3D-CATH Homeodomain-like UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
GTEx ENSG00000128645 GTEx
HGNC ID HGNC:5132 ENTREZGENE
Human Proteome Map HOXD1 Human Proteome Map
InterPro 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
  HXA1/B1/D1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report hsa:3231 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
NCBI Gene 3231 ENTREZGENE
OMIM 142987 OMIM
PANTHER HOMEOBOX PROTEIN HOX-D1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PTHR45946 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam Homeodomain UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PharmGKB PA29406 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 B2RAB4 ENTREZGENE
  HXD1_HUMAN UniProtKB/Swiss-Prot
  Q8IZ25_HUMAN UniProtKB/TrEMBL
  Q96CA4 ENTREZGENE, UniProtKB/TrEMBL
  Q9GZZ0 ENTREZGENE
UniProt Secondary B2RAB4 UniProtKB/Swiss-Prot