Rhox13 (Rhox homeobox family member 13) - Rat Genome Database

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Gene: Rhox13 (Rhox homeobox family member 13) Rattus norvegicus
Analyze
Symbol: Rhox13
Name: Rhox homeobox family member 13
RGD ID: 1586264
Description: Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific and RNA polymerase II transcription regulatory region sequence-specific DNA binding activity. Predicted to be involved in androgen receptor signaling pathway; positive regulation of gene expression; and regulation of transcription by RNA polymerase II. Predicted to act upstream of or within cellular response to retinoic acid. Predicted to be located in cytosol and nucleoplasm. Orthologous to human RHOXF1 (Rhox homeobox family member 1); INTERACTS WITH bisphenol A; 17beta-estradiol (ortholog); 5-aza-2'-deoxycytidine (ortholog).
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: homeobox protein Rhox13; LOC691244; rCG53272-like; Reproductive homeobox 13; similar to extraembryonic, spermatogenesis, homeobox 1-like
RGD Orthologs
Human
Mouse
Alliance Orthologs
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8X121,776,875 - 121,783,406 (+)NCBIGRCr8
mRatBN7.2X116,911,226 - 116,917,758 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 EnsemblX116,911,329 - 116,917,644 (+)EnsemblmRatBN7.2 Ensembl
Rnor_6.0X124,267,991 - 124,274,290 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 EnsemblX124,268,129 - 124,274,157 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0X124,353,797 - 124,360,019 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4X7,216,949 - 7,222,704 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
CeleraX116,128,924 - 116,135,440 (+)NCBICelera
Cytogenetic MapXq35NCBI
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
cytosol  (ISO)
nucleoplasm  (ISO)
nucleus  (ISO)

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

Genomics

Comparative Map Data
Rhox13
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8X121,776,875 - 121,783,406 (+)NCBIGRCr8
mRatBN7.2X116,911,226 - 116,917,758 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 EnsemblX116,911,329 - 116,917,644 (+)EnsemblmRatBN7.2 Ensembl
Rnor_6.0X124,267,991 - 124,274,290 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 EnsemblX124,268,129 - 124,274,157 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0X124,353,797 - 124,360,019 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4X7,216,949 - 7,222,704 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
CeleraX116,128,924 - 116,135,440 (+)NCBICelera
Cytogenetic MapXq35NCBI
RHOXF1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38X120,109,051 - 120,120,438 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 EnsemblX120,109,051 - 120,245,267 (-)EnsemblGRCh38hg38GRCh38
GRCh37X119,243,009 - 119,249,823 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36X119,127,053 - 119,133,875 (-)NCBINCBI36Build 36hg18NCBI36
CeleraX119,708,916 - 119,715,939 (+)NCBICelera
Cytogenetic MapXq24NCBI
HuRefX108,694,949 - 108,701,800 (-)NCBIHuRef
CHM1_1X119,154,044 - 119,160,880 (-)NCBICHM1_1
T2T-CHM13v2.0X118,484,211 - 118,495,405 (-)NCBIT2T-CHM13v2.0
Rhox13
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39X37,210,059 - 37,218,850 (+)NCBIGRCm39GRCm39mm39
GRCm39 EnsemblX37,210,096 - 37,218,844 (+)EnsemblGRCm39 Ensembl
GRCm38X38,120,840 - 38,129,966 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 EnsemblX38,121,219 - 38,129,967 (+)EnsemblGRCm38mm10GRCm38
MGSCv37X35,474,017 - 35,483,143 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36X34,365,917 - 34,374,599 (+)NCBIMGSCv36mm8
CeleraX25,766,316 - 25,775,542 (+)NCBICelera
Cytogenetic MapXA3.3NCBI
cM MapX22.38NCBI

Variants

.
Variants in Rhox13
9 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:37
Count of miRNA genes:36
Interacting mature miRNAs:37
Transcripts:ENSRNOT00000035489
Prediction methods:Miranda, Pita, Rnahybrid
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
1598856Memor1Memory QTL 11.9exploratory behavior trait (VT:0010471)total horizontal distance resulting from voluntary locomotion in an experimental apparatus (CMO:0001443)X103312877148312877Rat
1598872Memor14Memory QTL 144.5exploratory behavior trait (VT:0010471)difference between time of physical contact/close proximity of test subject and social stimulus during sample phase and test phase (CMO:0002678)X93956491138956491Rat
1598809Memor15Memory QTL 154.4exploratory behavior trait (VT:0010471)difference between time of physical contact/close proximity of test subject and social stimulus during sample phase and test phase (CMO:0002678)X103312877148312877Rat
738025Stresp3Stress response QTL 34.610.0066stress-related behavior trait (VT:0010451)defensive burying - approachX100567703150256146Rat
61430Cia18Collagen induced arthritis QTL 183.1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)X14843113120568734Rat
738029Stresp2Stress response QTL 23.40.0004stress-related behavior trait (VT:0010451)defensive burying - approachX112934952138400867Rat
61431Cia19Collagen induced arthritis QTL 194.4joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)X65612192120568734Rat
5685004Bss104Bone structure and strength QTL 1043.9tibia area (VT:1000281)tibia area measurement (CMO:0001382)X113805422126975220Rat
10059603Bw174Body weight QTL 1743.40.025body mass (VT:0001259)body weight (CMO:0000012)X113937816152453651Rat
724551Glom1Glomerulus QTL 12.80.0004kidney glomerulus morphology trait (VT:0005325)count of superficial glomeruli not directly contacting the kidney surface (CMO:0001002)X75294106120294106Rat
1598837Memor13Memory QTL 133.2exploratory behavior trait (VT:0010471)difference between time of physical contact/close proximity of test subject and social stimulus during sample phase and test phase (CMO:0002678)X41052407146860749Rat


Expression

RNA-SEQ Expression

appendage
circulatory system
endoderm
mesenchyme
mesoderm
reproductive system
respiratory system
3 1 1 4 1 51 1

Sequence


Ensembl Acc Id: ENSRNOT00000035489   ⟹   ENSRNOP00000035168
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 EnsemblX116,911,329 - 116,917,644 (+)Ensembl
Rnor_6.0 EnsemblX124,268,129 - 124,274,157 (+)Ensembl
RefSeq Acc Id: NM_001408904   ⟹   NP_001395833
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8X121,776,875 - 121,783,406 (+)NCBI
mRatBN7.2X116,911,226 - 116,917,758 (+)NCBI
Protein Sequences
Protein RefSeqs NP_001395833 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDM10856 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000035168.6
Ensembl Acc Id: ENSRNOP00000035168   ⟸   ENSRNOT00000035489
RefSeq Acc Id: NP_001395833   ⟸   NM_001408904
- UniProtKB: F1M524 (UniProtKB/TrEMBL)
Protein Domains
Homeobox

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-F1M524-F1-model_v2 AlphaFold F1M524 1-233 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:1586264 AgrOrtholog
BioCyc Gene G2FUF-1265 BioCyc
Ensembl Genes ENSRNOG00000028050 Ensembl, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000035489.6 UniProtKB/TrEMBL
Gene3D-CATH Homeodomain-like UniProtKB/TrEMBL
InterPro Homeobox_CS UniProtKB/TrEMBL
  Homeodomain UniProtKB/TrEMBL
  Homeodomain-like UniProtKB/TrEMBL
  Paired_Homeobox_TFs UniProtKB/TrEMBL
NCBI Gene 691244 ENTREZGENE
PANTHER HOMEOBOX PROTEIN ARISTALESS UniProtKB/TrEMBL
  HOMEOBOX PROTEIN RHOX13 UniProtKB/TrEMBL
Pfam Homeobox UniProtKB/TrEMBL
PhenoGen Rhox13 PhenoGen
PROSITE HOMEOBOX_1 UniProtKB/TrEMBL
  HOMEOBOX_2 UniProtKB/TrEMBL
RatGTEx ENSRNOG00000028050 RatGTEx
SMART HOX UniProtKB/TrEMBL
Superfamily-SCOP Homeodomain_like UniProtKB/TrEMBL
UniProt F1M524 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2017-07-14 Rhox13  Rhox homeobox family member 13  Rhox13  Reproductive homeobox 13  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2013-05-24 Rhox13  Reproductive homeobox 13  LOC100364841  rCG53272-like  Data merged from RGD:2320224 1643240 APPROVED
2010-05-05 LOC100364841  rCG53272-like      Symbol and Name status set to provisional 70820 PROVISIONAL
2008-09-18 Rhox13  Reproductive homeobox 13  LOC691244  similar to extraembryonic, spermatogenesis, homeobox 1-like  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-01-09 LOC691244  similar to extraembryonic, spermatogenesis, homeobox 1-like  LOC683136  similar to extraembryonic, spermatogenesis, homeobox 1-like  Data merged from RGD:1590430 1643240 APPROVED
2006-11-20 LOC683136  similar to extraembryonic, spermatogenesis, homeobox 1-like      Symbol and Name status set to provisional 70820 PROVISIONAL
2006-11-19 LOC691244  similar to extraembryonic, spermatogenesis, homeobox 1-like      Symbol and Name status set to provisional 70820 PROVISIONAL