Hoxd13 (homeo box D13) - Rat Genome Database

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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 nucleoplasm. 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
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8379,978,077 - 79,981,393 (+)NCBIGRCr8
mRatBN7.2359,570,647 - 59,573,963 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl359,570,646 - 59,573,963 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx362,957,898 - 62,961,202 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0371,541,543 - 71,544,847 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0369,306,624 - 69,309,926 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0361,590,376 - 61,593,692 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl361,590,376 - 61,593,692 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0368,056,713 - 68,060,029 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4357,283,682 - 57,286,998 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1357,180,052 - 57,181,906 (+)NCBI
Celera359,093,007 - 59,096,323 (+)NCBICelera
Cytogenetic Map3q23NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


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

Cellular Component
nucleoplasm  (IEA,ISO)
nucleus  (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 (+)NCBIGRCr8
mRatBN7.2359,570,647 - 59,573,963 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl359,570,646 - 59,573,963 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx362,957,898 - 62,961,202 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0371,541,543 - 71,544,847 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0369,306,624 - 69,309,926 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0361,590,376 - 61,593,692 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl361,590,376 - 61,593,692 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0368,056,713 - 68,060,029 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4357,283,682 - 57,286,998 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1357,180,052 - 57,181,906 (+)NCBI
Celera359,093,007 - 59,096,323 (+)NCBICelera
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 (+)EnsemblGRCh38hg38GRCh38
GRCh372176,957,449 - 176,960,672 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 362176,665,778 - 176,668,912 (+)NCBINCBI36Build 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 Ensembl
GRCm38274,668,225 - 74,671,603 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl274,668,310 - 74,671,599 (+)EnsemblGRCm38mm10GRCm38
MGSCv37274,506,367 - 74,509,655 (+)NCBIGRCm37MGSCv37mm9NCBIm37
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 (-)EnsemblChiLan1.0
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_Tasha
ROS_Cfam_1.03620,041,503 - 20,044,951 (+)NCBIROS_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_1.0
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 (+)EnsemblSpeTri2.0SpeTri2.0 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 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
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 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
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_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462478713,233,932 - 13,237,210 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Hoxd13
13 total Variants
miRNA Target Status

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 (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
2290452Scl56Serum cholesterol level QTL 562.26blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)3191609953Rat
1358905Hrtrt17Heart rate QTL 175.90.000014heart pumping trait (VT:2000009)heart rate (CMO:0000002)31086191289878372Rat
1358885Bp251Blood pressure QTL 2513.8arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)314489145121056321Rat
1358888Bp264Blood pressure QTL 2644.43arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)314489145121056321Rat
2298542Neuinf11Neuroinflammation QTL 113.9nervous system integrity trait (VT:0010566)spinal cord complement component 1, q subcomponent, B chain mRNA level (CMO:0002126)31500542276927699Rat
631676Cm8Cardiac mass QTL 87.030.0001aorta mass (VT:0002845)aorta weight (CMO:0000076)31695470861954708Rat
10450804Scl70Serum cholesterol level QTL 704.70.001blood LDL cholesterol amount (VT:0000181)blood low density lipoprotein cholesterol level (CMO:0000053)32071409065714090Rat
10450794Scl69Serum cholesterol level QTL 696.30.001blood LDL cholesterol amount (VT:0000181)blood low density lipoprotein cholesterol level (CMO:0000053)32071409065714090Rat
2302055Pia30Pristane induced arthritis QTL 303.50.001blood autoantibody amount (VT:0003725)serum immunoglobulin M-type rheumatoid factor level relative to an arbitrary reference serum (CMO:0002111)32793691972936919Rat
9590286Uminl1Urine mineral level QTL 13.50.001urine mineral amount (VT:0015086)urine electrolyte level (CMO:0000593)32824968773249687Rat
8694196Abfw2Abdominal fat weight QTL 216.580.001visceral adipose mass (VT:0010063)abdominal fat pad weight to body weight ratio (CMO:0000095)32824968773249687Rat
8694386Bw159Body weight QTL 1594.520.001body lean mass (VT:0010483)lean tissue morphological measurement (CMO:0002184)32824968773249687Rat
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)32824968773249687Rat
9590136Scort3Serum corticosterone level QTL 323.370.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)32824968773249687Rat
2303593Gluco46Glucose level QTL 463blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)32846857173468571Rat
1354590Despr11Despair related QTL 110.000031locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)32846857173468571Rat
737818Hcar12Hepatocarcinoma resistance QTL 122.6liver integrity trait (VT:0010547)volume of individual liver tumorous lesion (CMO:0001078)329463235118376539Rat
61419Cia11Collagen induced arthritis QTL 115.6joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)33035677398535386Rat
61356Bp37Blood pressure QTL 373blood pressure trait (VT:0000183)systolic blood pressure (CMO:0000004)33068464275684642Rat
631647Bp122Blood pressure QTL 1226.2arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)33068464275684642Rat
70216Cm14Cardiac mass QTL 142.1heart mass (VT:0007028)heart wet weight (CMO:0000069)331172320163586636Rat
11565451Bw177Body weight QTL 1770.002body mass (VT:0001259)body weight (CMO:0000012)33142640370668733Rat
11565452Kidm57Kidney mass QTL 570.001kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)33142640370668733Rat
12879866Cm94Cardiac mass QTL 940.001heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)33142640370668733Rat
12879867Cm95Cardiac mass QTL 950.047heart right ventricle mass (VT:0007033)heart right ventricle weight to body weight ratio (CMO:0000914)33142640370668733Rat
12879868Am6Aortic mass QTL 60.001aorta mass (VT:0002845)aorta weight to aorta length to body weight ratio (CMO:0002722)33142640370668733Rat
2301400Cm68Cardiac mass QTL 680.001heart mass (VT:0007028)heart wet weight to body weight ratio (CMO:0002408)33142640370668733Rat
1300169Bp177Blood pressure QTL 1772.96arterial blood pressure trait (VT:2000000)blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)33370334761017857Rat
1354589Bw31Body weight QTL 313.3body mass (VT:0001259)body weight (CMO:0000012)33370334778196190Rat
1354604Bw36Body weight QTL 362.9body mass (VT:0001259)body weight (CMO:0000012)333703347104104347Rat
1358362Srcrt2Stress Responsive Cort QTL 22.78blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)338192233133483320Rat
738019Anxrr10Anxiety related response QTL 103.9exploratory behavior trait (VT:0010471)number of entries into a discrete space in an experimental apparatus (CMO:0000960)33851780383517803Rat
2302276Bw82Body weight QTL 824.32body mass (VT:0001259)body weight (CMO:0000012)33945463762951183Rat
1331777Bw24Body weight QTL 243.503body mass (VT:0001259)body weight (CMO:0000012)33945463789115240Rat
1331795Rf30Renal function QTL 303.708urine potassium amount (VT:0010539)urine potassium level (CMO:0000128)33945463789115240Rat
1354597Kidm13Kidney mass QTL 132.9kidney mass (VT:0002707)right kidney wet weight (CMO:0000082)341874578104104347Rat
2301970Bw81Body weight QTL 815.19body mass (VT:0001259)body weight (CMO:0000012)341874578155617519Rat
2301971Cm71Cardiac mass QTL 714.63heart left ventricle mass (VT:0007031)heart left ventricle weight (CMO:0000776)341874578155617519Rat
1300178Hrtrt4Heart rate QTL 43.74heart pumping trait (VT:2000009)heart rate (CMO:0000002)34382736490905114Rat
1581503Cm58Cardiac mass QTL 582.70.05heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)343827364121056321Rat
1559282Emca5Estrogen-induced mammary cancer QTL 53.9mammary gland integrity trait (VT:0010552)percentage of study population developing mammary tumors during a period of time (CMO:0000948)343827364169034231Rat
2292591Esta4Estrogen-induced thymic atrophy QTL 4thymus mass (VT:0004954)thymus wet weight (CMO:0000855)347233211147415807Rat
1358186Ept2Estrogen-induced pituitary tumorigenesis QTL 28.3pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)347233430110362260Rat
2292613Ept16Estrogen-induced pituitary tumorigenesis QTL 168.3pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)347233430110362260Rat
631665Bw8Body weight QTL 85.5body mass (VT:0001259)body weight (CMO:0000012)350437042119183768Rat
724523Tsu1Thymus enlargement suppressive QTL 13.84thymus mass (VT:0004954)thymus weight to body weight ratio (CMO:0000612)350437504115638231Rat
1582249Bw77Body weight QTL 773.20.0025epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)35318459364655484Rat
1582218Bw74Body weight QTL 743.90.0021body mass (VT:0001259)body weight (CMO:0000012)353184593115665732Rat
1582238Bw68Body weight QTL 683.20.0064body mass (VT:0001259)body weight (CMO:0000012)353184593115665732Rat
1582239Epfw1Epididymal fat weight QTL 14.50.0006epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)353184593115665732Rat
61377Edpm3Estrogen-dependent pituitary mass QTL 37.050.038pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)35318469289878207Rat
731180Bp152Blood pressure QTL 1520.03arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)35378111291609953Rat
731180Bp152Blood pressure QTL 1520.03arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)35378111291609953Rat
731180Bp152Blood pressure QTL 1520.03arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)35378111291609953Rat
1581568Rf53Renal function QTL 53urine total protein amount (VT:0000032)urine protein excretion rate to body weight ratio (CMO:0001099)356395968161299569Rat
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)359242096157323038Rat

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
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 hemolymphoid system integumental system musculoskeletal system renal system reproductive system appendage
High
Medium 2
Low 1 6 11
Below cutoff 1 2 2 2 2 3 9 10 2

Sequence


RefSeq Acc Id: ENSRNOT00000002155   ⟹   ENSRNOP00000002155
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
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:
RefSeq 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
  ENSRNOT00000002155.5 UniProtKB/TrEMBL
Gene3D-CATH Homeodomain-like UniProtKB/TrEMBL
InterPro 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