Hoxd13 (homeo box D13) - Rat Genome Database

Send us a Message
Submit Data |  Help |  Video Tutorials |  News |  Publications |  Download |  REST API |  Citing RGD |  Contact   
Search RGD Grant Resources Citing RGD About Us Contact Us
Genes Variants Community Projects QTLs Strains Markers Genome Information Ontologies Cell Lines References Download Submit Data
OntoMate (Literature Search) JBrowse (Genome Browser) Synteny Browser (VCMap) Variant Visualizer Multi-Ontology Enrichment (MOET) Gene-Ortholog Location Finder (GOLF) InterViewer (Protein-Protein Interactions) PhenoMiner (Quatitative Phenotypes) Gene Annotator OLGA (Gene List Generator) AllianceMine GViewer (Genome Viewer)
Aging & Age-Related Disease Behavioral & Substance Use Disorder Cancer & Neoplastic Disease Cardiovascular Disease Coronavirus Disease Developmental Disease Diabetes Hematologic Disease Immune & Inflammatory Disease Infectious Disease Liver Disease Neurological Disease Obesity & Metabolic Syndrome Renal Disease Respiratory Disease Sensory Organ Disease
Find Models Genetic Models Autism Models Rat PhenoMiner (Quantitative Phenotypes) Chinchilla PhenoMiner Expected Ranges (Quantitative Phenotype) PhenoMiner Term Comparison Hybrid Rat Diversity Panel Phenotypes Phenotypes in Other Animal Models Animal Husbandry Strain Medical Records Phylogenetics Strain Availability Calendar Rats 101 Submissions Photo Archive
Pathways
Rat Community Forum Directory of Rat Laboratories Video Tutorials News RGD Publications RGD Presentations Archive Nomenclature Guidelines Resource Links Laboratory Resources Employment Resources
Advanced Search (OLGA)
Gene: Hoxd13 (homeo box D13) Rattus norvegicus
Analyze
Symbol: Hoxd13
Name: homeo box D13
RGD ID: 1308417
Description: Enables sequence-specific double-stranded DNA binding activity. Involved in embryonic hindgut morphogenesis; prostate gland development; and response to testosterone. Predicted to be located in nucleus. Biomarker of hypospadias. Human ortholog(s) of this gene implicated in brachydactyly-syndactyly syndrome; clubfoot; cryptorchidism; and dysostosis (multiple). Orthologous to human HOXD13 (homeobox D13); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; bisphenol A; dibutyl phthalate.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: homeobox protein Hox-D13; LOC288154
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Black Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8379,978,077 - 79,981,393 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl379,978,076 - 79,981,393 (+)EnsemblGRCr8
mRatBN7.2359,570,647 - 59,573,963 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl359,570,646 - 59,573,963 (+)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx362,957,898 - 62,961,202 (+)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0371,541,543 - 71,544,847 (+)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0369,306,624 - 69,309,926 (+)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0361,590,376 - 61,593,692 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl361,590,376 - 61,593,692 (+)Ensemblrn6Rnor6.0
Rnor_5.0368,056,713 - 68,060,029 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.4357,283,682 - 57,286,998 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera359,093,007 - 59,096,323 (+)NCBICelera
RGSC_v3.1357,180,052 - 57,181,906 (+)NCBI
Cytogenetic Map3q23NCBI
JBrowse:




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

Cellular Component
nucleus  (IEA,ISO)

References

References - curated
# Reference Title Reference Citation
1. Genomic structure of HOXD13 gene: a nine polyalanine duplication causes synpolydactyly in two unrelated families. Akarsu AN, etal., Hum Mol Genet. 1996 Jul;5(7):945-52.
2. The mouse Hoxd13(spdh) mutation, a polyalanine expansion similar to human type II synpolydactyly (SPD), disrupts the function but not the expression of other Hoxd genes. Bruneau S, etal., Dev Biol. 2001 Sep 15;237(2):345-53.
3. The expression of Gli3, regulated by HOXD13, may play a role in idiopathic congenital talipes equinovarus. Cao D, etal., BMC Musculoskelet Disord. 2009 Nov 19;10:142. doi: 10.1186/1471-2474-10-142.
4. An I47L substitution in the HOXD13 homeodomain causes a novel human limb malformation by producing a selective loss of function. Caronia G, etal., Development. 2003 Apr;130(8):1701-12.
5. Mutation analysis of HOXD13 gene in a Chinese pedigree with synpolydactyly. Dai L, etal., Zhonghua Yi Xue Yi Chuan Xue Za Zhi. 2005 Jun;22(3):277-80.
6. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
7. Rat ISS GO annotations from GOA human gene data--August 2006 GOA data from the GO Consortium
8. Synpolydactyly phenotypes correlate with size of expansions in HOXD13 polyalanine tract. Goodman FR, etal., Proc Natl Acad Sci U S A. 1997 Jul 8;94(14):7458-63.
9. Posterior Hox gene expression and differential androgen regulation in the developing and adult rat prostate lobes. Huang L, etal., Endocrinology. 2007 Mar;148(3):1235-45. Epub 2006 Nov 30.
10. Isolated brachydactyly type E caused by a HOXD13 nonsense mutation: a case report. Jamsheer A, etal., BMC Med Genet. 2012 Jan 10;13:4. doi: 10.1186/1471-2350-13-4.
11. Missense mutations in the homeodomain of HOXD13 are associated with brachydactyly types D and E. Johnson D, etal., Am J Hum Genet. 2003 Apr;72(4):984-97. Epub 2003 Mar 14.
12. A nonsense mutation in the HOXD13 gene underlies synpolydactyly with incomplete penetrance. Kurban M, etal., J Hum Genet. 2011 Oct;56(10):701-6. doi: 10.1038/jhg.2011.84. Epub 2011 Aug 4.
13. Sonic hedgehog, BMP4, and Hox genes in the development of anorectal malformations in Ethylenethiourea-exposed fetal rats. Mandhan P, etal., J Pediatr Surg. 2006 Dec;41(12):2041-5.
14. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
15. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
16. GOA pipeline RGD automated data pipeline
17. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
18. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
19. Comprehensive gene review and curation RGD comprehensive gene curation
20. A splice donor site mutation in HOXD13 underlies synpolydactyly with cortical bone thinning. Shi X, etal., Gene. 2013 Dec 15;532(2):297-301. doi: 10.1016/j.gene.2013.09.040. Epub 2013 Sep 18.
21. A novel non-synonymous mutation in the homeodomain of HOXD13 causes synpolydactyly in a Chinese family. Wang B, etal., Clin Chim Acta. 2012 Jul 11;413(13-14):1049-52. doi: 10.1016/j.cca.2012.02.015. Epub 2012 Feb 22.
22. Exome sequencing identifies a novel nonsense mutation of HOXD13 in a Chinese family with synpolydactyly. Wang B, etal., Congenit Anom (Kyoto). 2017 Jan;57(1):4-7. doi: 10.1111/cga.12173.
23. A hypermorphic mouse Gli3 allele results in a polydactylous limb phenotype. Wang C, etal., Dev Dyn. 2007 Mar;236(3):769-76.
24. [Analysis of association between 5' HOXD gene and idiopathic congenital talipes equinovarus]. Wang LL, etal., Zhonghua Yi Xue Yi Chuan Xue Za Zhi. 2005 Dec;22(6):653-6.
25. Allelic variants in HOX genes in cryptorchidism. Wang Y, etal., Birth Defects Res A Clin Mol Teratol. 2007 Apr;79(4):269-75.
26. Mutations in HOXD13 underlie syndactyly type V and a novel brachydactyly-syndactyly syndrome. Zhao X, etal., Am J Hum Genet. 2007 Feb;80(2):361-71. Epub 2007 Jan 3.
27. A novel mutation outside homeodomain of HOXD13 causes synpolydactyly in a Chinese family. Zhou X, etal., Bone. 2013 Nov;57(1):237-41. doi: 10.1016/j.bone.2013.07.039. Epub 2013 Aug 12.
28. Maternal exposure to di-n-butyl phthalate (DBP) induces combined anorectal and urogenital malformations in male rat offspring. Zhu YP, etal., Reprod Toxicol. 2016 Jun;61:169-76. doi: 10.1016/j.reprotox.2016.04.007. Epub 2016 Apr 11.
Additional References at PubMed
PMID:8106170   PMID:8620844   PMID:8900279   PMID:8978698   PMID:9097018   PMID:9342042   PMID:11850178   PMID:12668621   PMID:15617687   PMID:16314414   PMID:16672333   PMID:17714700  
PMID:19168674   PMID:23995701   PMID:24789103   PMID:26581570   PMID:26884828   PMID:27706137  


Genomics

Comparative Map Data
Hoxd13
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8379,978,077 - 79,981,393 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl379,978,076 - 79,981,393 (+)EnsemblGRCr8
mRatBN7.2359,570,647 - 59,573,963 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl359,570,646 - 59,573,963 (+)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx362,957,898 - 62,961,202 (+)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0371,541,543 - 71,544,847 (+)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0369,306,624 - 69,309,926 (+)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0361,590,376 - 61,593,692 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl361,590,376 - 61,593,692 (+)Ensemblrn6Rnor6.0
Rnor_5.0368,056,713 - 68,060,029 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.4357,283,682 - 57,286,998 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera359,093,007 - 59,096,323 (+)NCBICelera
RGSC_v3.1357,180,052 - 57,181,906 (+)NCBI
Cytogenetic Map3q23NCBI
HOXD13
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh382176,087,487 - 176,095,944 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl2176,092,721 - 176,095,944 (+)Ensemblhg38GRCh38
GRCh372176,957,449 - 176,960,672 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 362176,665,778 - 176,668,912 (+)NCBIBuild 36Build 36hg18NCBI36
Build 342176,783,038 - 176,785,307NCBI
Celera2170,566,680 - 170,569,816 (+)NCBICelera
Cytogenetic Map2q31.1NCBI
HuRef2168,835,017 - 168,838,150 (+)NCBIHuRef
CHM1_12176,963,384 - 176,966,518 (+)NCBICHM1_1
T2T-CHM13v2.02176,580,842 - 176,584,065 (+)NCBIT2T-CHM13v2.0
Hoxd13
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39274,498,569 - 74,501,947 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl274,498,654 - 74,501,943 (+)EnsemblGRCm39 EnsemblGRCm39
GRCm38274,668,225 - 74,671,603 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl274,668,310 - 74,671,599 (+)Ensemblmm10GRCm38
MGSCv37274,506,367 - 74,509,655 (+)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv36274,469,149 - 74,470,975 (+)NCBIMGSCv36mm8
Celera276,338,416 - 76,341,706 (+)NCBICelera
Cytogenetic Map2C3NCBI
cM Map244.13NCBI
Hoxd13
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495540320,568,314 - 20,575,579 (-)Ensembl
ChiLan1.0NW_00495540320,568,314 - 20,575,579 (-)NCBIChiLan1.0ChiLan1.0
HOXD13
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v21378,760,254 - 78,763,474 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan12B78,775,230 - 78,778,450 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v02B63,372,517 - 63,375,731 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.12B181,081,518 - 181,085,295 (+)NCBIPanPan1.1PanPan1.1panPan2
HOXD13
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.13619,901,184 - 19,903,837 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha3619,910,345 - 19,913,770 (+)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.03620,041,503 - 20,044,951 (+)NCBIROS_Cfam_1.0ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl3620,041,322 - 20,044,660 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.13620,115,748 - 20,119,177 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.03620,116,491 - 20,119,912 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.03620,228,239 - 20,231,674 (+)NCBIUU_Cfam_GSD_1.0UU_Cfam_GSD_1.0
Hoxd13
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024405303137,025,943 - 137,028,811 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049365095,579,843 - 5,581,651 (+)EnsemblSpeTri2.0 Ensembl
SpeTri2.0NW_0049365095,579,846 - 5,581,651 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
HOXD13
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1581,893,972 - 81,896,944 (+)EnsemblsusScr11Sscrofa11.1
Sscrofa11.11581,893,997 - 81,897,965 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21591,361,348 - 91,364,513 (+)NCBISscrofa10.2Sscrofa10.2susScr3
HOXD13
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11061,662,670 - 61,670,955 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl1061,667,880 - 61,669,743 (+)EnsemblChlSab1.1 EnsemblchlSab2Vervet-AGM
Vero_WHO_p1.0NW_023666040137,939,510 - 137,942,856 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Hoxd13
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462478713,233,932 - 13,238,503 (+)EnsemblHetGla_female_1.0 EnsemblhetGla2HetGla_female_1.0 Ensembl
HetGla 1.0NW_00462478713,233,932 - 13,237,210 (+)NCBIHetGla 1.0HetGla 1.0hetGla2
Hoxd13
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v1552,009,533 - 52,012,820 (+)NCBIRrattus_CSIRO_v1

Variants

.
Variants in Hoxd13
33 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:651
Count of miRNA genes:273
Interacting mature miRNAs:335
Transcripts:ENSRNOT00000002155
Prediction methods:Microtar, Miranda, 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.


QTLs in Region (GRCr8)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1300178Hrtrt4Heart rate QTL 43.74heart pumping trait (VT:2000009)heart rate (CMO:0000002)351490129111359995Rat
61377Edpm3Estrogen-dependent pituitary mass QTL 37.050.038pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)373592611110333156Rat
1358293Bw38Body weight QTL 3860.0000031body mass (VT:0001259)body weight (CMO:0000012)374364268119364268Rat
1582238Bw68Body weight QTL 683.20.0064body mass (VT:0001259)body weight (CMO:0000012)373592512136118980Rat
1331795Rf30Renal function QTL 303.708urine potassium amount (VT:0010539)urine potassium level (CMO:0000128)35986366387321459Rat
1582239Epfw1Epididymal fat weight QTL 14.50.0006epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)373592512136118980Rat
70216Cm14Cardiac mass QTL 142.1heart mass (VT:0007028)heart wet weight (CMO:0000069)351581665184004958Rat
1354589Bw31Body weight QTL 313.3body mass (VT:0001259)body weight (CMO:0000012)35365182698651826Rat
2303593Gluco46Glucose level QTL 463blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)34887661993876619Rat
1354590Despr11Despair related QTL 110.000031locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)34887661993876619Rat
2298542Neuinf11Neuroinflammation QTL 113.9nervous system integrity trait (VT:0010566)spinal cord complement component 1, q subcomponent, B chain mRNA level (CMO:0002126)33540319997383526Rat
2292591Esta4Estrogen-induced thymic atrophy QTL 4thymus mass (VT:0004954)thymus wet weight (CMO:0000855)367641776167835660Rat
1358362Srcrt2Stress Responsive Cort QTL 22.78blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)358601291153936591Rat
631832Sach1Saccharin preference QTL 12.70.02consumption behavior trait (VT:0002069)calculated saccharin drink intake volume (CMO:0001600)34790417292904172Rat
737818Hcar12Hepatocarcinoma resistance QTL 122.6liver integrity trait (VT:0010547)volume of individual liver tumorous lesion (CMO:0001078)349872657138829559Rat
1582218Bw74Body weight QTL 743.90.0021body mass (VT:0001259)body weight (CMO:0000012)373592512136118980Rat
1331777Bw24Body weight QTL 243.503body mass (VT:0001259)body weight (CMO:0000012)35986366387321459Rat
631647Bp122Blood pressure QTL 1226.2arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)35109256196092561Rat
1300169Bp177Blood pressure QTL 1772.96arterial blood pressure trait (VT:2000000)blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)33642511681425116Rat
9590286Uminl1Urine mineral level QTL 13.50.001urine mineral amount (VT:0015086)urine electrolyte level (CMO:0000593)34865774493657744Rat
724523Tsu1Thymus enlargement suppressive QTL 13.84thymus mass (VT:0004954)thymus weight to body weight ratio (CMO:0000612)370845569136091483Rat
4889966Bss95Bone structure and strength QTL 954.4tibia area (VT:1000281)tibia-fibula cross-sectional area (CMO:0001718)33779691982796919Rat
8662816Vetf4Vascular elastic tissue fragility QTL 44renal artery integrity trait (VT:0010642)number of ruptures of the internal elastic lamina of the renal arteries (CMO:0002563)379649560177741895Rat
2302276Bw82Body weight QTL 824.32body mass (VT:0001259)body weight (CMO:0000012)35986366383358329Rat
2292613Ept16Estrogen-induced pituitary tumorigenesis QTL 168.3pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)367641995130815812Rat
738019Anxrr10Anxiety related response QTL 103.9exploratory behavior trait (VT:0010471)number of entries into a discrete space in an experimental apparatus (CMO:0000960)358925062103925062Rat
631841Niddm39Non-insulin dependent diabetes mellitus QTL 393.36blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)370311536115311536Rat
9590136Scort3Serum corticosterone level QTL 323.370.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)34865774493657744Rat
61419Cia11Collagen induced arthritis QTL 115.6joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)35076614595766145Rat
61356Bp37Blood pressure QTL 373blood pressure trait (VT:0000183)systolic blood pressure (CMO:0000004)35109256196092561Rat
1358905Hrtrt17Heart rate QTL 175.90.000014heart pumping trait (VT:2000009)heart rate (CMO:0000002)336721849110333156Rat
1558650Cm48Cardiac mass QTL 4840.0001heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)35076614595766145Rat
8694196Abfw2Abdominal fat weight QTL 216.580.001visceral adipose mass (VT:0010063)abdominal fat pad weight to body weight ratio (CMO:0000095)34865774493657744Rat
1358885Bp251Blood pressure QTL 2513.8arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)31141509147Rat
1354597Kidm13Kidney mass QTL 132.9kidney mass (VT:0002707)right kidney wet weight (CMO:0000082)342158111124558371Rat
1582249Bw77Body weight QTL 773.20.0025epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)37359251285062403Rat
2325840Bp345Blood pressure QTL 3450.001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)33870893183708931Rat
8552950Pigfal12Plasma insulin-like growth factor 1 level QTL 127.3blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)34865774493657744Rat
631676Cm8Cardiac mass QTL 87.030.0001aorta mass (VT:0002845)aorta weight (CMO:0000076)33736373482363734Rat
2290452Scl56Serum cholesterol level QTL 562.26blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)33610140381101403Rat
8694386Bw159Body weight QTL 1594.520.001body lean mass (VT:0010483)lean tissue morphological measurement (CMO:0002184)34865774493657744Rat
1354604Bw36Body weight QTL 362.9body mass (VT:0001259)body weight (CMO:0000012)342158111124558371Rat
1358888Bp264Blood pressure QTL 2644.43arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)35675975141509147Rat
1358186Ept2Estrogen-induced pituitary tumorigenesis QTL 28.3pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)367641995130815812Rat

Markers in Region
Hoxd13  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2359,571,097 - 59,572,388 (+)MAPPERmRatBN7.2
Rnor_6.0361,590,827 - 61,592,117NCBIRnor6.0
Rnor_5.0368,057,164 - 68,058,454UniSTSRnor5.0
RGSC_v3.4357,284,133 - 57,285,423UniSTSRGSC3.4
Celera359,093,458 - 59,094,748UniSTS
Cytogenetic Map3q23UniSTS
Hoxd13  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2359,572,259 - 59,572,493 (+)MAPPERmRatBN7.2
Rnor_6.0361,591,989 - 61,592,222NCBIRnor6.0
Rnor_5.0368,058,326 - 68,058,559UniSTSRnor5.0
RGSC_v3.4357,285,295 - 57,285,528UniSTSRGSC3.4
Celera359,094,620 - 59,094,853UniSTS
Cytogenetic Map3q23UniSTS


Expression

RNA-SEQ Expression

alimentary part of gastrointestinal system
appendage
circulatory system
ectoderm
endocrine system
endoderm
exocrine system
hemolymphoid system
hepatobiliary system
integumental system
mesenchyme
mesoderm
musculoskeletal system
nervous system
renal system
reproductive system
respiratory system
sensory system
visual system
15 3 5 7 6 5 3 3 3 1 61 14 1 4 27 49 2 1 1

Sequence


Ensembl Acc Id: ENSRNOT00000002155   ⟹   ENSRNOP00000002155
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl379,978,076 - 79,981,393 (+)Ensembl
mRatBN7.2 Ensembl359,570,646 - 59,573,963 (+)Ensembl
Rnor_6.0 Ensembl361,590,376 - 61,593,692 (+)Ensembl
RefSeq Acc Id: NM_001105886   ⟹   NP_001099356
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8379,978,077 - 79,981,393 (+)NCBI
mRatBN7.2359,570,647 - 59,573,963 (+)NCBI
Rnor_6.0361,590,376 - 61,593,692 (+)NCBI
Rnor_5.0368,056,713 - 68,060,029 (+)NCBI
RGSC_v3.4357,283,682 - 57,286,998 (+)RGD
Celera359,093,007 - 59,096,323 (+)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_001099356 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDL79178 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000002155
  ENSRNOP00000002155.4
RefSeq Acc Id: NP_001099356   ⟸   NM_001105886
- UniProtKB: A6HMC7 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000002155   ⟸   ENSRNOT00000002155
Protein Domains
Homeobox

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D4ACD0-F1-model_v2 AlphaFold D4ACD0 1-331 view protein structure

Transcriptome

eQTL   View at Phenogen
WGCNA   View at Phenogen
Tissue/Strain Expression   View at Phenogen


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1308417 AgrOrtholog
BioCyc Gene G2FUF-49335 BioCyc
Ensembl Genes ENSRNOG00000001588 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000002155 ENTREZGENE
  ENSRNOT00000002155.6 UniProtKB/TrEMBL
Gene3D-CATH Homeodomain-like UniProtKB/TrEMBL
InterPro AP_axis_regulatory_Homeobox UniProtKB/TrEMBL
  Homeobox UniProtKB/TrEMBL
  Homeobox_CS UniProtKB/TrEMBL
  Homeodomain-like UniProtKB/TrEMBL
  HoxA13_N UniProtKB/TrEMBL
KEGG Report rno:288154 UniProtKB/TrEMBL
NCBI Gene 288154 ENTREZGENE
PANTHER HOMEOBOX PROTEIN HOX-D13 UniProtKB/TrEMBL
  SEGMENTATION PROTEIN FUSHI TARAZU-LIKE PROTEIN UniProtKB/TrEMBL
Pfam Homeobox UniProtKB/TrEMBL
  HoxA13_N UniProtKB/TrEMBL
PhenoGen Hoxd13 PhenoGen
PROSITE HOMEOBOX_1 UniProtKB/TrEMBL
  HOMEOBOX_2 UniProtKB/TrEMBL
RatGTEx ENSRNOG00000001588 RatGTEx
SMART HOX UniProtKB/TrEMBL
Superfamily-SCOP Homeodomain_like UniProtKB/TrEMBL
UniProt A6HMC7 ENTREZGENE, UniProtKB/TrEMBL
  D4ACD0_RAT UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-04-30 Hoxd13  homeo box D13   Hoxd13_predicted  homeo box D13 (predicted)  'predicted' is removed 2292626 APPROVED
2005-01-12 Hoxd13_predicted  homeo box D13 (predicted)      Symbol and Name status set to approved 70820 APPROVED