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 Genes
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


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
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


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


RefSeq Acc Id: ENSRNOT00000080456   ⟹   ENSRNOP00000073361
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl361,604,672 - 61,606,400 (+)Ensembl
RefSeq 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
RefSeq Acc Id: ENSRNOP00000073361   ⟸   ENSRNOT00000080456
RefSeq Acc Id: ENSRNOP00000097759   ⟸   ENSRNOT00000114347
RefSeq Acc Id: NP_001414331   ⟸   NM_001427402
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, ENTREZGENE, 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_RAT 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