Arx (aristaless related homeobox) - Rat Genome Database

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Gene: Arx (aristaless related homeobox) Rattus norvegicus
Analyze
Symbol: Arx
Name: aristaless related homeobox
RGD ID: 1562672
Description: Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific; RNA polymerase II cis-regulatory region sequence-specific DNA binding activity; and chromatin binding activity. Involved in neuron development. Predicted to be located in nucleus. Biomarker of type 2 diabetes mellitus. Human ortholog(s) of this gene implicated in X-linked lissencephaly 2; X-linked recessive disease (multiple); corpus callosum agenesis-abnormal genitalia syndrome; and syndromic X-linked intellectual disability Hedera type. Orthologous to human ARX (aristaless related homeobox); INTERACTS WITH 6-propyl-2-thiouracil; alpha-Zearalanol; Cuprizon.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: aristaless related homeobox gene (Drosophila); aristaless-related homeobox; homeobox protein ARX; LOC317268; RGD1562672; similar to Arx homeoprotein
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
GRCr8X62,010,097 - 62,022,009 (+)NCBIGRCr8
mRatBN7.2X58,016,233 - 58,028,149 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 EnsemblX58,016,233 - 58,028,142 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_UtxX59,442,698 - 59,454,605 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0X62,943,813 - 62,955,718 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0X60,501,842 - 60,513,757 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0X62,363,757 - 62,376,139 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 EnsemblX62,363,757 - 62,376,143 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0X62,957,562 - 62,969,944 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4X80,631,375 - 80,643,989 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
CeleraX58,455,664 - 58,467,636 (+)NCBICelera
Cytogenetic MapXq22NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component
nucleus  (IEA,ISO)

References

References - curated
# Reference Title Reference Citation
1. ARX, a novel Prd-class-homeobox gene highly expressed in the telencephalon, is mutated in X-linked mental retardation. Bienvenu T, etal., Hum Mol Genet. 2002 Apr 15;11(8):981-91.
2. The c.429_452 duplication of the ARX gene: a unique developmental-model of limb kinetic apraxia. Curie A, etal., Orphanet J Rare Dis. 2014 Feb 14;9:25. doi: 10.1186/1750-1172-9-25.
3. Cell-autonomous roles of ARX in cell proliferation and neuronal migration during corticogenesis. Friocourt G, etal., J Neurosci. 2008 May 28;28(22):5794-805. doi: 10.1523/JNEUROSCI.1067-08.2008.
4. 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.
5. Expansion of the first PolyA tract of ARX causes infantile spasms and status dystonicus. Guerrini R, etal., Neurology. 2007 Jul 31;69(5):427-33.
6. Three human ARX mutations cause the lissencephaly-like and mental retardation with epilepsy-like pleiotropic phenotypes in mice. Kitamura K, etal., Hum Mol Genet. 2009 Oct 1;18(19):3708-24. doi: 10.1093/hmg/ddp318. Epub 2009 Jul 15.
7. Mutation of ARX causes abnormal development of forebrain and testes in mice and X-linked lissencephaly with abnormal genitalia in humans. Kitamura K, etal., Nat Genet. 2002 Nov;32(3):359-69. Epub 2002 Oct 15.
8. Targeted loss of Arx results in a developmental epilepsy mouse model and recapitulates the human phenotype in heterozygous females. Marsh E, etal., Brain. 2009 Jun;132(Pt 6):1563-76. doi: 10.1093/brain/awp107. Epub 2009 May 12.
9. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
10. Limited role for SREBP-1c in defective glucose-induced insulin secretion from Zucker diabetic fatty rat islets: a functional and gene profiling analysis. Parton LE, etal., Am J Physiol Endocrinol Metab. 2006 Nov;291(5):E982-94. Epub 2006 Jun 13.
11. Neuroanatomical distribution of ARX in brain and its localisation in GABAergic neurons. Poirier K, etal., Brain Res Mol Brain Res. 2004 Mar 17;122(1):35-46.
12. A triplet repeat expansion genetic mouse model of infantile spasms syndrome, Arx(GCG)10+7, with interneuronopathy, spasms in infancy, persistent seizures, and adult cognitive and behavioral impairment. Price MG, etal., J Neurosci. 2009 Jul 8;29(27):8752-63. doi: 10.1523/JNEUROSCI.0915-09.2009.
13. GOA pipeline RGD automated data pipeline
14. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
15. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
16. Comprehensive gene review and curation RGD comprehensive gene curation
17. X-linked myoclonic epilepsy with spasticity and intellectual disability: mutation in the homeobox gene ARX. Scheffer IE, etal., Neurology. 2002 Aug 13;59(3):348-56.
18. XLMR in MRX families 29, 32, 33 and 38 results from the dup24 mutation in the ARX (Aristaless related homeobox) gene. Stepp ML, etal., BMC Med Genet. 2005 Apr 25;6:16.
Additional References at PubMed
PMID:15677725   PMID:15930104   PMID:16301625   PMID:17460091   PMID:21966449   PMID:22387004   PMID:23246292   PMID:34871948  


Genomics

Comparative Map Data
Arx
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8X62,010,097 - 62,022,009 (+)NCBIGRCr8
mRatBN7.2X58,016,233 - 58,028,149 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 EnsemblX58,016,233 - 58,028,142 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_UtxX59,442,698 - 59,454,605 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0X62,943,813 - 62,955,718 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0X60,501,842 - 60,513,757 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0X62,363,757 - 62,376,139 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 EnsemblX62,363,757 - 62,376,143 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0X62,957,562 - 62,969,944 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4X80,631,375 - 80,643,989 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
CeleraX58,455,664 - 58,467,636 (+)NCBICelera
Cytogenetic MapXq22NCBI
ARX
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38X25,003,694 - 25,015,965 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 EnsemblX25,003,694 - 25,016,420 (-)EnsemblGRCh38hg38GRCh38
GRCh37X25,021,811 - 25,034,082 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36X24,932,213 - 24,943,775 (-)NCBINCBI36Build 36hg18NCBI36
Build 34X24,781,948 - 24,793,511NCBI
CeleraX29,145,744 - 29,157,998 (-)NCBICelera
Cytogenetic MapXp21.3NCBI
HuRefX22,763,568 - 22,793,924 (-)NCBIHuRef
CHM1_1X25,053,346 - 25,065,599 (-)NCBICHM1_1
T2T-CHM13v2.0X24,587,932 - 24,600,202 (-)NCBIT2T-CHM13v2.0
Arx
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39X92,330,113 - 92,341,963 (+)NCBIGRCm39GRCm39mm39
GRCm39 EnsemblX92,330,051 - 92,341,963 (+)EnsemblGRCm39 Ensembl
GRCm38X93,286,507 - 93,298,357 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 EnsemblX93,286,445 - 93,298,357 (+)EnsemblGRCm38mm10GRCm38
MGSCv37X90,531,985 - 90,543,696 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36X89,539,365 - 89,551,076 (+)NCBIMGSCv36mm8
CeleraX80,208,596 - 80,220,179 (+)NCBICelera
Cytogenetic MapXC3NCBI
cM MapX41.05NCBI
Arx
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0NW_0049555095,326,145 - 5,338,250 (-)NCBIChiLan1.0ChiLan1.0
ARX
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2X26,800,416 - 26,814,128 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1X26,803,792 - 26,817,510 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0X17,598,858 - 17,612,544 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1X24,965,203 - 24,977,939 (-)NCBIpanpan1.1PanPan1.1panPan2
ARX
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1X20,545,346 - 20,556,206 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 EnsemblX20,545,346 - 20,556,206 (-)EnsemblCanFam3.1canFam3CanFam3.1
ROS_Cfam_1.0X20,498,344 - 20,511,419 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 EnsemblX20,499,238 - 20,510,100 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1X20,538,249 - 20,549,126 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0X20,571,748 - 20,582,617 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0X20,628,835 - 20,639,715 (-)NCBIUU_Cfam_GSD_1.0
Arx
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2X13,532,367 - 13,551,810 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_004936836295,664 - 306,756 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_004936836295,090 - 306,756 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
ARX
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 EnsemblX21,067,621 - 21,079,723 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1X21,067,631 - 21,079,850 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2X22,463,824 - 22,474,788 (-)NCBISscrofa10.2Sscrofa10.2susScr3
ARX
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1X23,499,791 - 23,518,333 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 EnsemblX23,500,454 - 23,511,524 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366605625,363,945 - 25,376,208 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Arx
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046248971,279,138 - 1,303,210 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Arx
16 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:428
Count of miRNA genes:233
Interacting mature miRNAs:273
Transcripts:ENSRNOT00000049655
Prediction methods:Microtar, Miranda, 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
61430Cia18Collagen induced arthritis QTL 183.1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)X14843113120568734Rat
71116Niddm16Non-insulin dependent diabetes mellitus QTL 167.81blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)X1529780260297802Rat
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
738035Stresp1Stress response QTL 14.960.000011stress-related behavior trait (VT:0010451)defensive burying - copingX41304447112935181Rat
70221Bp56Blood pressure QTL 564.9arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)X5704214165612192Rat

Markers in Region
RH128932  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2X58,027,922 - 58,028,121 (+)MAPPERmRatBN7.2
Rnor_6.0X62,375,913 - 62,376,111NCBIRnor6.0
Rnor_5.0X62,969,718 - 62,969,916UniSTSRnor5.0
RGSC_v3.4X80,643,763 - 80,643,961UniSTSRGSC3.4
CeleraX58,467,410 - 58,467,608UniSTS
RH 3.4 Map6627.1UniSTS
Cytogenetic MapXq22UniSTS
Arx  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2X58,027,247 - 58,028,120 (+)MAPPERmRatBN7.2
Rnor_6.0X62,375,238 - 62,376,110NCBIRnor6.0
Rnor_5.0X62,969,043 - 62,969,915UniSTSRnor5.0
RGSC_v3.4X80,643,088 - 80,643,960UniSTSRGSC3.4
CeleraX58,466,735 - 58,467,607UniSTS
Cytogenetic MapXq22UniSTS
UniSTS:532310  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2X58,027,706 - 58,028,120 (+)MAPPERmRatBN7.2
Rnor_6.0X62,375,697 - 62,376,110NCBIRnor6.0
Rnor_5.0X62,969,502 - 62,969,915UniSTSRnor5.0
CeleraX58,467,194 - 58,467,607UniSTS
Cytogenetic MapXq22UniSTS


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 endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium 1 44 22
Low 1 1 8 10 22 16 8
Below cutoff 2 11 7 13 7 2 2 7

Sequence


RefSeq Acc Id: ENSRNOT00000083362   ⟹   ENSRNOP00000075250
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 EnsemblX62,363,953 - 62,375,185 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000089828   ⟹   ENSRNOP00000071239
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 EnsemblX58,016,233 - 58,028,142 (+)Ensembl
Rnor_6.0 EnsemblX62,366,453 - 62,376,143 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000091240   ⟹   ENSRNOP00000068900
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 EnsemblX62,363,757 - 62,365,855 (+)Ensembl
RefSeq Acc Id: NM_001100174   ⟹   NP_001093644
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8X62,010,097 - 62,022,009 (+)NCBI
mRatBN7.2X58,016,233 - 58,028,149 (+)NCBI
Rnor_6.0X62,363,757 - 62,376,139 (+)NCBI
Rnor_5.0X62,957,562 - 62,969,944 (+)NCBI
RGSC_v3.4X80,631,375 - 80,643,989 (+)RGD
CeleraX58,455,664 - 58,467,636 (+)RGD
Sequence:
RefSeq Acc Id: NP_001093644   ⟸   NM_001100174
- UniProtKB: A6YP92 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSRNOP00000071239   ⟸   ENSRNOT00000089828
RefSeq Acc Id: ENSRNOP00000068900   ⟸   ENSRNOT00000091240
RefSeq Acc Id: ENSRNOP00000075250   ⟸   ENSRNOT00000083362
Protein Domains
Homeobox   OAR

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-A6YP92-F1-model_v2 AlphaFold A6YP92 1-566 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:1562672 AgrOrtholog
BioCyc Gene G2FUF-2268 BioCyc
Ensembl Genes ENSRNOG00000053562 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  ENSRNOG00055030029 UniProtKB/Swiss-Prot
  ENSRNOG00060015194 UniProtKB/Swiss-Prot
  ENSRNOG00065010046 UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000089828 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOT00000089828.2 UniProtKB/Swiss-Prot
  ENSRNOT00055052063 UniProtKB/Swiss-Prot
  ENSRNOT00060026049 UniProtKB/Swiss-Prot
  ENSRNOT00065016166 UniProtKB/Swiss-Prot
Gene3D-CATH Homeodomain-like UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
InterPro Homeobox-like_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Homeobox_CS UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Homeobox_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  OAR_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:317268 UniProtKB/Swiss-Prot
NCBI Gene 317268 ENTREZGENE
PANTHER ARISTALESS-RELATED HOMEOBOX PROTEIN-RELATED UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  HOMEOBOX PROTEIN ARISTALESS UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam Homeodomain UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  OAR UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Arx PhenoGen
PROSITE HOMEOBOX_1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  HOMEOBOX_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  OAR UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
RatGTEx ENSRNOG00000053562 RatGTEx
  ENSRNOG00055030029 RatGTEx
  ENSRNOG00060015194 RatGTEx
  ENSRNOG00065010046 RatGTEx
SMART HOX UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF46689 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A0A0G2JZZ1_RAT UniProtKB/TrEMBL
  A6YP92 ENTREZGENE, UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-09-25 Arx  aristaless related homeobox  Arx  aristaless related homeobox gene (Drosophila)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-02-29 Arx  aristaless related homeobox gene (Drosophila)  RGD1562672_predicted  similar to Arx homeoprotein (predicted)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-03-07 RGD1562672_predicted  similar to Arx homeoprotein (predicted)  LOC317268  similar to Arx homeoprotein  Symbol and Name status set to approved 1299863 APPROVED
2006-02-09 LOC317268  similar to Arx homeoprotein      Symbol and Name status set to provisional 70820 PROVISIONAL