Hoxd11 (homeobox D11) - Rat Genome Database

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Gene: Hoxd11 (homeobox D11) Rattus norvegicus
Analyze
Symbol: Hoxd11
Name: homeobox D11
RGD ID: 7730597
Description: Predicted to enable 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 several processes, including embryonic morphogenesis; kidney development; and regionalization. Predicted to be located in nucleoplasm. Orthologous to human HOXD11 (homeobox D11); INTERACTS WITH flusilazole; 1,2-dichloroethane (ortholog); 17beta-hydroxy-5alpha-androstan-3-one (ortholog).
Type: protein-coding
RefSeq Status: INFERRED
Previously known as: homeobox protein Hox-D11; LOC102553842; uncharacterized LOC102553842
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Pig
Green Monkey
Alliance Orthologs
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8379,992,394 - 79,994,688 (+)NCBIGRCr8
mRatBN7.2359,584,840 - 59,587,257 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl359,585,039 - 59,586,783 (+)EnsemblmRatBN7.2 Ensembl
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
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component
nucleoplasm  (IEA,ISO)

Molecular Function

References

References - curated
# Reference Title Reference Citation
1. 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.
2. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
3. Abnormalities of vertebral formation and Hox expression in congenital kyphoscoliotic rats. Seki T, etal., Mol Cell Biochem. 2008 May;312(1-2):193-9. doi: 10.1007/s11010-008-9734-4. Epub 2008 Mar 9.
Additional References at PubMed
PMID:7925020   PMID:8900279   PMID:11493536   PMID:12050119   PMID:12869760   PMID:14668414   PMID:17714700   PMID:20978074   PMID:22916278   PMID:23760953  


Genomics

Comparative Map Data
Hoxd11
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8379,992,394 - 79,994,688 (+)NCBIGRCr8
mRatBN7.2359,584,840 - 59,587,257 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl359,585,039 - 59,586,783 (+)EnsemblmRatBN7.2 Ensembl
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
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh382176,107,280 - 176,115,679 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl2176,104,216 - 176,109,754 (+)EnsemblGRCh38hg38GRCh38
GRCh372176,972,008 - 176,974,482 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 362176,680,330 - 176,682,562 (+)NCBINCBI36Build 36hg18NCBI36
Build 342176,797,590 - 176,799,823NCBI
Celera2170,581,234 - 170,583,461 (+)NCBICelera
Cytogenetic Map2q31.1NCBI
HuRef2168,849,568 - 168,851,540 (+)NCBIHuRef
CHM1_12176,977,935 - 176,980,184 (+)NCBICHM1_1
T2T-CHM13v2.02176,595,402 - 176,599,952 (+)NCBIT2T-CHM13v2.0
Hoxd11
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39274,509,902 - 74,517,360 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl274,509,901 - 74,517,360 (+)EnsemblGRCm39 Ensembl
GRCm38274,679,558 - 74,687,016 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl274,679,557 - 74,687,016 (+)EnsemblGRCm38mm10GRCm38
MGSCv37274,520,450 - 74,522,195 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36274,483,232 - 74,484,977 (+)NCBIMGSCv36mm8
Celera276,352,501 - 76,354,246 (+)NCBICelera
Cytogenetic Map2C3NCBI
cM Map244.13NCBI
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
NHGRI_mPanPan1-v21378,774,821 - 78,780,697 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan12B78,789,797 - 78,792,163 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v02B63,386,806 - 63,398,777 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.12B181,095,347 - 181,098,680 (+)NCBIpanpan1.1PanPan1.1panPan2
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 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.03620,052,553 - 20,060,228 (+)NCBIROS_Cfam_1.0
UMICH_Zoey_3.13620,129,998 - 20,134,442 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.03620,130,689 - 20,135,144 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.03620,239,278 - 20,246,796 (+)NCBIUU_Cfam_GSD_1.0
HOXD11
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1581,908,460 - 81,911,282 (+)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 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl1061,682,400 - 61,684,168 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_023666040137,925,780 - 137,928,157 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0

Variants

.
Variants in Hoxd11
9 total Variants

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


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 hemolymphoid system integumental system musculoskeletal system renal system reproductive system appendage
High
Medium 20 12
Low 2 15 14
Below cutoff 1 2 2 6 2

Sequence


Ensembl Acc Id: ENSRNOT00000080456   ⟹   ENSRNOP00000073361
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl361,604,672 - 61,606,400 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000114347   ⟹   ENSRNOP00000097759
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl359,585,039 - 59,586,783 (+)Ensembl
RefSeq Acc Id: NM_001427402   ⟹   NP_001414331
RefSeq Status: INFERRED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8379,992,394 - 79,994,688 (+)NCBI
Protein Sequences
Protein RefSeqs NP_001414331 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000097759.1
Ensembl Acc Id: ENSRNOP00000073361   ⟸   ENSRNOT00000080456
Ensembl Acc Id: ENSRNOP00000097759   ⟸   ENSRNOT00000114347
RefSeq Acc Id: NP_001414331   ⟸   NM_001427402
- UniProtKB: A0A8I6AT90 (UniProtKB/TrEMBL)
Protein Domains
Homeobox

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-A0A0G2K5B2-F1-model_v2 AlphaFold A0A0G2K5B2 1-327 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:7730597 AgrOrtholog
BioCyc Gene G2FUF-49333 BioCyc
Ensembl Genes ENSRNOG00000051472 Ensembl
  ENSRNOG00000069591 Ensembl, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000114347.1 UniProtKB/TrEMBL
Gene3D-CATH Homeodomain-like UniProtKB/TrEMBL
InterPro DUF3528 UniProtKB/TrEMBL
  Homeobox-like_sf UniProtKB/TrEMBL
  Homeobox_CS UniProtKB/TrEMBL
  Homeobox_dom UniProtKB/TrEMBL
  Homeobox_metazoa UniProtKB/TrEMBL
NCBI Gene LOC102553842 ENTREZGENE
PANTHER HOMEOBOX PROTEIN HOX-A11-RELATED UniProtKB/TrEMBL
  HOMEOBOX PROTEIN HOX-D11 UniProtKB/TrEMBL
Pfam DUF3528 UniProtKB/TrEMBL
  Homeodomain UniProtKB/TrEMBL
PhenoGen Hoxd11 PhenoGen
PRINTS HOMEOBOX UniProtKB/TrEMBL
PROSITE HOMEOBOX_1 UniProtKB/TrEMBL
  HOMEOBOX_2 UniProtKB/TrEMBL
RatGTEx ENSRNOG00000051472 RatGTEx
  ENSRNOG00000069591 RatGTEx
SMART HOX UniProtKB/TrEMBL
Superfamily-SCOP SSF46689 UniProtKB/TrEMBL
UniProt A0A8I6AT90 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2022-06-02 Hoxd11  homeobox D11  Hoxd11  homeobox D11  Data merged from RGD:149736300 737654 PROVISIONAL
2021-08-09 Hoxd11  homeobox D11      Symbol and Name status set to provisional 45752 PROVISIONAL
2015-06-08 Hoxd11  homeobox D11  LOC102553842  uncharacterized LOC102553842  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2013-12-18 LOC102553842  uncharacterized LOC102553842      Symbol and Name status set to provisional 70820 PROVISIONAL