Hmx1 (H6 family homeobox 1) - Rat Genome Database

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Gene: Hmx1 (H6 family homeobox 1) Rattus norvegicus
Analyze
Symbol: Hmx1
Name: H6 family homeobox 1
RGD ID: 1304928
Description: Predicted to enable DNA-binding transcription repressor activity, RNA polymerase II-specific and RNA polymerase II transcription regulatory region sequence-specific DNA binding activity. Predicted to be involved in negative regulation of transcription by RNA polymerase II. Predicted to be active in nucleus. Human ortholog(s) of this gene implicated in oculoauricular syndrome. Orthologous to human HMX1 (H6 family homeobox 1); INTERACTS WITH 2,2',4,4'-Tetrabromodiphenyl ether; 2,3,7,8-tetrachlorodibenzodioxine; 6-propyl-2-thiouracil.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: H6 homeo box 1; homeobox protein HMX1; LOC360960
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81479,585,840 - 79,589,626 (-)NCBIGRCr8
mRatBN7.21475,361,207 - 75,364,993 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1475,361,225 - 75,364,993 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1479,814,609 - 79,818,392 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01481,055,478 - 81,059,261 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01477,500,481 - 77,504,264 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01480,540,558 - 80,544,607 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1480,541,075 - 80,544,342 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01480,166,228 - 80,170,223 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41480,995,410 - 80,999,166 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11480,998,296 - 81,006,796 (-)NCBI
Celera1474,289,521 - 74,293,302 (-)NCBICelera
Cytogenetic Map14q21NCBI
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

Cellular Component
nucleus  (IBA)

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. Rat ISS GO annotations from GOA human gene data--August 2006 GOA data from the GO Consortium
3. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
4. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
5. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:9628823   PMID:10206974   PMID:22736458  


Genomics

Comparative Map Data
Hmx1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81479,585,840 - 79,589,626 (-)NCBIGRCr8
mRatBN7.21475,361,207 - 75,364,993 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1475,361,225 - 75,364,993 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1479,814,609 - 79,818,392 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01481,055,478 - 81,059,261 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01477,500,481 - 77,504,264 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01480,540,558 - 80,544,607 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1480,541,075 - 80,544,342 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01480,166,228 - 80,170,223 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41480,995,410 - 80,999,166 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11480,998,296 - 81,006,796 (-)NCBI
Celera1474,289,521 - 74,293,302 (-)NCBICelera
Cytogenetic Map14q21NCBI
HMX1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh3848,846,076 - 8,871,839 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl48,846,076 - 8,871,839 (-)EnsemblGRCh38hg38GRCh38
GRCh3748,847,802 - 8,873,565 (-)NCBIGRCh37GRCh37hg19GRCh37
Celera48,752,103 - 8,753,019 (-)NCBICelera
Cytogenetic Map4p16.1NCBI
CHM1_148,866,719 - 8,871,490 (-)NCBICHM1_1
T2T-CHM13v2.048,812,981 - 8,838,746 (-)NCBIT2T-CHM13v2.0
Hmx1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39535,546,124 - 35,557,629 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl535,546,452 - 35,557,074 (+)EnsemblGRCm39 Ensembl
GRCm38535,388,780 - 35,400,285 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl535,389,108 - 35,399,730 (+)EnsemblGRCm38mm10GRCm38
MGSCv37535,731,766 - 35,735,521 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36535,705,978 - 35,709,733 (+)NCBIMGSCv36mm8
Celera532,864,491 - 32,868,246 (+)NCBICelera
Cytogenetic Map5B3NCBI
cM Map518.14NCBI
Hmx1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0NW_0049555142,441,234 - 2,442,478 (+)NCBIChiLan1.0ChiLan1.0
HMX1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v239,133,528 - 9,138,423 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan149,062,172 - 9,067,067 (-)NCBINHGRI_mPanPan1
HMX1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1360,503,149 - 60,506,799 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl360,503,149 - 60,506,799 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha363,154,635 - 63,158,286 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0360,979,862 - 60,983,513 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl360,979,862 - 60,983,513 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1360,474,226 - 60,477,877 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0360,679,465 - 60,683,123 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0361,035,384 - 61,039,035 (-)NCBIUU_Cfam_GSD_1.0
Hmx1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440528566,257,094 - 66,260,965 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_00493647719,959,376 - 19,962,663 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_00493647719,958,786 - 19,962,657 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
HMX1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl82,440,876 - 2,444,846 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.182,440,727 - 2,445,549 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.284,641,131 - 4,651,143 (+)NCBISscrofa10.2Sscrofa10.2susScr3
HMX1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12744,761,393 - 44,774,447 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl2744,766,485 - 44,770,394 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_0236660511,089,695 - 1,115,900 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Hmx1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462475524,208,666 - 24,210,576 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Hmx1
10 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:350
Count of miRNA genes:198
Interacting mature miRNAs:227
Transcripts:ENSRNOT00000012304
Prediction methods:Microtar, Miranda, Rnahybrid, 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
2313089Bss81Bone structure and strength QTL 813.40.0001body length (VT:0001256)body length, nose to rump (CMO:0000079)143766971982669719Rat
9590294Uminl4Urine mineral level QTL 45.660.001urine mineral amount (VT:0015086)urine electrolyte level (CMO:0000593)1455624247100624247Rat
1582236Gluco22Glucose level QTL 223.30.0164blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)147341532392554092Rat
2300197Scl59Serum cholesterol level QTL 59blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)1455147478100147478Rat
70214Niddm28Non-insulin dependent diabetes mellitus QTL 284.06blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)143999825175582726Rat
70153Bp59Blood pressure QTL 593.2arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)146875779683368335Rat
70187Pancm5Pancreatic morphology QTL 516.7pancreas mass (VT:0010144)pancreas weight to body weight ratio (CMO:0000630)143032009280829842Rat
631523Pia13Pristane induced arthritis QTL 133.3joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)144079346098037301Rat
1582259Gluco23Glucose level QTL 233.10.0008blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)1470053989104886043Rat
1582197Gluco27Glucose level QTL 273.40.0006blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)147341532392554092Rat
2313100Bss82Bone structure and strength QTL 8230.0001tibia size trait (VT:0100001)tibia midshaft cross-sectional area (CMO:0001717)143766971982669719Rat
634328Hc5Hypercalciuria QTL 52.3urine calcium amount (VT:0002985)urine calcium excretion rate (CMO:0000763)1458184885103184885Rat
1582250Gluco26Glucose level QTL 263.30.0009blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)147341532395876975Rat
2317879Alcrsp27Alcohol response QTL 273.30.63response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)1456631369101631369Rat
1641900Alcrsp11Alcohol response QTL 11alcohol metabolism trait (VT:0015089)blood ethanol level (CMO:0000535)1470053989104886043Rat
631839Niddm37Non-insulin dependent diabetes mellitus QTL 373.37blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)141103062295876975Rat
1582255Gluco29Glucose level QTL 293.10.0025blood glucose amount (VT:0000188)absolute change in blood glucose level area under curve (CMO:0002034)147341532392554092Rat
9589034Epfw11Epididymal fat weight QTL 1160.001epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)1455624247100624247Rat
1582209Gluco20Glucose level QTL 203.80.0005blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)147341532392554092Rat
2313048Bss84Bone structure and strength QTL 843.10.0001tibia strength trait (VT:1000284)tibia total energy absorbed before break (CMO:0001736)143766971982669719Rat
1300136Rf22Renal function QTL 223.9renal blood flow trait (VT:2000006)absolute change in renal vascular resistance (CMO:0001900)144226252995023211Rat
1549834Scl45Serum cholesterol level QTL 455.8blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)145002321195023211Rat
738037Hcas6Hepatocarcinoma susceptibility QTL 62.93liver integrity trait (VT:0010547)liver nonremodeling tumorous lesion volume to total liver volume ratio (CMO:0001464)143905723783368335Rat
2313084Bss83Bone structure and strength QTL 832.90.0001tibia size trait (VT:0100001)tibia midshaft endosteal cross-sectional area (CMO:0001716)143766971982669719Rat

Markers in Region
RH139641  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21475,361,412 - 75,361,626 (+)MAPPERmRatBN7.2
Rnor_6.01480,540,764 - 80,540,977NCBIRnor6.0
Rnor_5.01480,166,434 - 80,166,647UniSTSRnor5.0
RGSC_v3.41480,995,598 - 80,995,811UniSTSRGSC3.4
Celera1474,289,709 - 74,289,922UniSTS
Cytogenetic Map14q21UniSTS
RH140508  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21475,361,271 - 75,361,436 (+)MAPPERmRatBN7.2
Rnor_6.01480,540,623 - 80,540,787NCBIRnor6.0
Rnor_5.01480,166,293 - 80,166,457UniSTSRnor5.0
RGSC_v3.41480,995,457 - 80,995,621UniSTSRGSC3.4
Celera1474,289,568 - 74,289,732UniSTS
Cytogenetic Map14q21UniSTS


Expression

RNA-SEQ Expression

appendage
circulatory system
ectoderm
endocrine system
endoderm
exocrine system
hemolymphoid system
hepatobiliary system
integumental system
mesenchyme
mesoderm
nervous system
renal system
reproductive system
respiratory system
1 6 26 24 14 3 3 3 6 42 18 12 20 51 11

Sequence


Ensembl Acc Id: ENSRNOT00000012304   ⟹   ENSRNOP00000012304
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1475,361,225 - 75,364,993 (-)Ensembl
Rnor_6.0 Ensembl1480,541,075 - 80,544,342 (-)Ensembl
RefSeq Acc Id: NM_001108363   ⟹   NP_001101833
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81479,585,840 - 79,589,626 (-)NCBI
mRatBN7.21475,361,207 - 75,364,993 (-)NCBI
Rnor_6.01480,540,576 - 80,544,345 (-)NCBI
Rnor_5.01480,166,228 - 80,170,223 (-)NCBI
RGSC_v3.41480,995,410 - 80,999,166 (-)RGD
Celera1474,289,521 - 74,293,302 (-)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_001101833 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDM00063 (Get FASTA)   NCBI Sequence Viewer  
  EDM00064 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000012304.5
RefSeq Acc Id: NP_001101833   ⟸   NM_001108363
- UniProtKB: D3ZBP8 (UniProtKB/TrEMBL),   A6IJZ9 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000012304   ⟸   ENSRNOT00000012304
Protein Domains
Homeobox

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D3ZBP8-F1-model_v2 AlphaFold D3ZBP8 1-333 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:1304928 AgrOrtholog
BioCyc Gene G2FUF-15319 BioCyc
Ensembl Genes ENSRNOG00000009154 Ensembl, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000012304.6 UniProtKB/TrEMBL
Gene3D-CATH Homeodomain-like UniProtKB/TrEMBL
InterPro HMX_Homeobox_TF UniProtKB/TrEMBL
  Homeobox UniProtKB/TrEMBL
  Homeobox_CS UniProtKB/TrEMBL
  Homeobox_region UniProtKB/TrEMBL
  Homeodomain-like UniProtKB/TrEMBL
KEGG Report rno:360960 UniProtKB/TrEMBL
NCBI Gene 360960 ENTREZGENE
PANTHER HOMEOBOX PROTEIN HMX UniProtKB/TrEMBL
  HOMEOBOX PROTEIN HMX1 UniProtKB/TrEMBL
Pfam Homeobox UniProtKB/TrEMBL
PhenoGen Hmx1 PhenoGen
PRINTS HOMEOBOX UniProtKB/TrEMBL
PROSITE HOMEOBOX_1 UniProtKB/TrEMBL
  HOMEOBOX_2 UniProtKB/TrEMBL
RatGTEx ENSRNOG00000009154 RatGTEx
SMART HOX UniProtKB/TrEMBL
Superfamily-SCOP Homeodomain_like UniProtKB/TrEMBL
UniProt A6IJZ9 ENTREZGENE, UniProtKB/TrEMBL
  A6IK00_RAT UniProtKB/TrEMBL
  D3ZBP8 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-09-24 Hmx1  H6 family homeobox 1  Hmx1  H6 homeo box 1   Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-04-30 Hmx1  H6 homeo box 1   Hmx1_predicted  H6 homeo box 1 (predicted)  'predicted' is removed 2292626 APPROVED
2005-01-12 Hmx1_predicted  H6 homeo box 1 (predicted)      Symbol and Name status set to approved 70820 APPROVED