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 have DNA-binding transcription repressor activity, RNA polymerase II-specific; RNA polymerase II cis-regulatory region sequence-specific DNA binding activity; and chromatin binding activity. Involved in brain development and neuron development. Localizes to nucleus. Biomarker of type 2 diabetes mellitus. Human ortholog(s) of this gene implicated in Partington syndrome; early infantile epileptic encephalopathy 1; lissencephaly; and syndromic X-linked intellectual disability Hedera type. Orthologous to human ARX (aristaless related homeobox); INTERACTS WITH 6-propyl-2-thiouracil; dibutyl phthalate; fenvalerate.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: aristaless related homeobox gene (Drosophila); aristaless-related homeobox; homeobox protein ARX; LOC317268; RGD1562672; similar to Arx homeoprotein
Orthologs:
Homo sapiens (human) : ARX (aristaless related homeobox)  HGNC  Alliance
Mus musculus (house mouse) : Arx (aristaless related homeobox)  MGI  Alliance
Chinchilla lanigera (long-tailed chinchilla) : Arx (aristaless related homeobox)
Pan paniscus (bonobo/pygmy chimpanzee) : ARX (aristaless related homeobox)
Canis lupus familiaris (dog) : ARX (aristaless related homeobox)
Ictidomys tridecemlineatus (thirteen-lined ground squirrel) : Arx (aristaless related homeobox)
Sus scrofa (pig) : ARX (aristaless related homeobox)
Chlorocebus sabaeus (African green monkey) : ARX (aristaless related homeobox)
Heterocephalus glaber (naked mole-rat) : Arx (aristaless related homeobox)
more info ...
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
NCBI Annotation Information: Annotation category: suggests misassembly; Annotation category: partial on reference assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
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 (+)NCBIRGSC3.4rn4RGSC3.4
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
chromatin  (IBA)
nucleus  (IDA,IEA)

References

Additional References at PubMed
PMID:15677725   PMID:15930104   PMID:16301625   PMID:17460091   PMID:21966449   PMID:22387004   PMID:23246292  


Genomics

Comparative Map Data
Arx
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
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 (+)NCBIRGSC3.4rn4RGSC3.4
CeleraX58,455,664 - 58,467,636 (+)NCBICelera
Cytogenetic MapXq22NCBI
ARX
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 EnsemblX25,003,694 - 25,016,420 (-)EnsemblGRCh38hg38GRCh38
GRCh38X25,003,694 - 25,015,965 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh37X25,021,811 - 25,034,065 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36X24,932,213 - 24,943,775 (-)NCBINCBI36hg18NCBI36
Build 34X24,781,948 - 24,793,511NCBI
CeleraX29,145,744 - 29,157,998 (-)NCBI
Cytogenetic MapXp21.3NCBI
HuRefX22,763,568 - 22,793,924 (-)NCBIHuRef
CHM1_1X25,053,346 - 25,065,599 (-)NCBICHM1_1
Arx
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39X92,330,113 - 92,341,963 (+)NCBI
GRCm38X93,286,507 - 93,298,357 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 EnsemblX93,286,445 - 93,298,357 (+)EnsemblGRCm38mm10GRCm38
MGSCv37X90,531,985 - 90,543,696 (+)NCBIGRCm37mm9NCBIm37
MGSCv36X89,539,365 - 89,551,076 (+)NCBImm8
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
PanPan1.1X24,965,203 - 24,977,939 (-)NCBIpanpan1.1PanPan1.1panPan2
Mhudiblu_PPA_v0X17,598,858 - 17,612,544 (-)NCBIMhudiblu_PPA_v0panPan3
ARX
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1 EnsemblX20,545,346 - 20,556,206 (-)EnsemblCanFam3.1canFam3CanFam3.1
CanFam3.1X20,545,346 - 20,556,206 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Arx
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
SpeTri2.0NW_004936836295,090 - 306,756 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
ARX
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 EnsemblX21,067,613 - 21,079,524 (-)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 - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1 EnsemblX23,500,454 - 23,511,524 (-)Ensembl
ChlSab1.1X23,499,791 - 23,518,333 (-)NCBI
Arx
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046248971,279,138 - 1,303,210 (-)NCBI

Position Markers
RH128932  
Rat AssemblyChrPosition (strand)SourceJBrowse
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
Cytogenetic MapXq22UniSTS
RH 3.4 Map6627.1UniSTS
Arx  
Rat AssemblyChrPosition (strand)SourceJBrowse
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
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


QTLs in Region (Rnor_6.0)
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)X15688119127888215Rat
71116Niddm16Non-insulin dependent diabetes mellitus QTL 167.81blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)X1815335263153352Rat
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)X44320616158345622Rat
738035Stresp1Stress response QTL 14.960.000011stress-related behavior trait (VT:0010451)defensive burying - copingX44557974120045269Rat
70221Bp56Blood pressure QTL 564.9arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)X6139809770352120Rat

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.


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


Reference Sequences
RefSeq Acc Id: ENSRNOT00000083362   ⟹   ENSRNOP00000075250
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 EnsemblX62,363,953 - 62,375,185 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000089828   ⟹   ENSRNOP00000071239
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 EnsemblX62,366,453 - 62,376,143 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000091240   ⟹   ENSRNOP00000068900
RefSeq Status:
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
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:
Protein Sequences
Protein RefSeqs NP_001093644 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein A6YP92 (Get FASTA)   NCBI Sequence Viewer  
  ABR27821 (Get FASTA)   NCBI Sequence Viewer  
  EDL96017 (Get FASTA)   NCBI Sequence Viewer  
  EDL96018 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
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

Transcriptome

eQTL   View at Phenogen
WGCNA   View at Phenogen
Tissue/Strain Expression   View at Phenogen


Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
ACI/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
ACI/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BBDP/Wor (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
BN/SsN (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
Buf/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
COP/CrCrl (MCW & UW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
University of Wisconsin (Dr. James Shull)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Charles River Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)
F344/NCrl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
F344/NRrrc (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
FHH/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHH/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FHL/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHL/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
GH/OmrMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
GK/Ox (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LE/Stm (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/Crl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/NCrlBR (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LH/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LL/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LN/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
M520/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
MHS/Gib (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MNS/Gib (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MR/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
SBH/Ygl (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBH/Ygl sequenced by MCW
SBH/Ygl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SBN/Ygl (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBN/Ygl sequenced by MCW
SBN/Ygl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/NHsd (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHRSP/Gcrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SR/JrHsd (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/Jr (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/JrHsdMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SS/JrHsdMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/Rij (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/Gcrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
WKY/NCrl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WN/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1562672 AgrOrtholog
Ensembl Genes ENSRNOG00000053562 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000068900 UniProtKB/TrEMBL
  ENSRNOP00000071239 UniProtKB/TrEMBL
  ENSRNOP00000075250 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000083362 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOT00000089828 UniProtKB/TrEMBL
  ENSRNOT00000091240 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
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
SMART HOX UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF46689 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniGene Rn.22484 ENTREZGENE
UniProt A0A0G2JTZ4_RAT UniProtKB/TrEMBL
  A0A0G2JZZ1_RAT UniProtKB/TrEMBL
  A0A0G2KA42_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