Armcx4 (armadillo repeat containing, X-linked 4) - Rat Genome Database
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Gene: Armcx4 (armadillo repeat containing, X-linked 4) Rattus norvegicus
Analyze
Symbol: Armcx4
Name: armadillo repeat containing, X-linked 4
RGD ID: 2325053
Description: Predicted to localize to integral component of membrane. Orthologous to human ARMCX4 (armadillo repeat containing X-linked 4); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; bisphenol A; oxaliplatin.
Type: protein-coding
RefSeq Status: MODEL
Also known as: armadillo repeat-containing X-linked protein 4; LOC100359678
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2X97,860,526 - 97,870,912 (+)NCBI
Rnor_6.0 EnsemblX105,500,173 - 105,507,288 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0X105,497,277 - 105,507,636 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0X105,386,682 - 105,396,989 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4X122,141,844 - 122,149,307 (+)NCBIRGSC3.4rn4RGSC3.4
CeleraX98,900,961 - 98,911,320 (+)NCBICelera
Cytogenetic MapXq32NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Function

References

Additional References at PubMed
PMID:31904090  


Genomics

Comparative Map Data
Armcx4
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2X97,860,526 - 97,870,912 (+)NCBI
Rnor_6.0 EnsemblX105,500,173 - 105,507,288 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0X105,497,277 - 105,507,636 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0X105,386,682 - 105,396,989 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4X122,141,844 - 122,149,307 (+)NCBIRGSC3.4rn4RGSC3.4
CeleraX98,900,961 - 98,911,320 (+)NCBICelera
Cytogenetic MapXq32NCBI
ARMCX4
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 EnsemblX101,418,287 - 101,533,459 (+)EnsemblGRCh38hg38GRCh38
GRCh38X101,418,278 - 101,535,988 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh37X100,673,064 - 100,790,975 (+)NCBIGRCh37GRCh37hg19GRCh37
GRCh37X100,673,266 - 100,790,975 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36X100,559,939 - 100,587,809 (+)NCBINCBI36hg18NCBI36
Build 34X100,546,606 - 100,594,591NCBI
CeleraX101,192,724 - 101,307,940 (+)NCBI
Cytogenetic MapXq22.1NCBI
HuRefX90,479,139 - 90,599,050 (+)NCBIHuRef
CHM1_1X100,566,789 - 100,684,815 (+)NCBICHM1_1
Armcx4
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39X133,586,399 - 133,598,524 (+)NCBIGRCm39mm39
GRCm38X134,685,650 - 134,697,775 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 EnsemblX134,686,519 - 134,696,757 (+)EnsemblGRCm38mm10GRCm38
MGSCv37X131,221,058 - 131,231,296 (+)NCBIGRCm37mm9NCBIm37
MGSCv36X130,035,695 - 130,066,008 (+)NCBImm8
CeleraX117,566,650 - 117,578,175 (+)NCBICelera
Cytogenetic MapXE3NCBI
Armcx4
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049555037,606,353 - 7,613,363 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049555037,603,395 - 7,613,711 (+)NCBIChiLan1.0ChiLan1.0
ARMCX4
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1X100,752,524 - 100,865,613 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 EnsemblX100,818,769 - 100,825,467 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0X90,683,100 - 90,735,935 (+)NCBIMhudiblu_PPA_v0panPan3
ARMCX4
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1 EnsemblX75,397,802 - 75,405,301 (+)EnsemblCanFam3.1canFam3CanFam3.1
CanFam3.1X75,394,315 - 75,412,888 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Armcx4
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
SpeTri2.0NW_004936813540,574 - 557,845 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
ARMCX4
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 EnsemblX83,092,682 - 83,103,838 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1X83,092,592 - 83,130,725 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
ARMCX4
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1X89,814,215 - 89,824,819 (+)NCBI
ChlSab1.1 EnsemblX89,816,747 - 89,824,998 (+)Ensembl
Armcx4
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046249021,075,902 - 1,085,596 (-)NCBI


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
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
61431Cia19Collagen induced arthritis QTL 194.4joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)X70352120127888215Rat
724551Glom1Glomerulus QTL 12.80.0004kidney glomerulus morphology trait (VT:0005325)count of superficial glomeruli not directly contacting the kidney surface (CMO:0001002)X82930791127930791Rat
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)X101333032146333032Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:101
Count of miRNA genes:94
Interacting mature miRNAs:98
Transcripts:ENSRNOT00000040476
Prediction methods:Microtar, Miranda, Pita, 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.


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 circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium 26 8 6 6 1 1 70 21 33 3 1
Low 3 17 49 35 19 35 7 10 4 14 3 8 7
Below cutoff 5

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000040476   ⟹   ENSRNOP00000051224
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 EnsemblX105,500,173 - 105,507,288 (+)Ensembl
RefSeq Acc Id: XM_006227438   ⟹   XP_006227500
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
CeleraX98,900,961 - 98,911,320 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006227439   ⟹   XP_006227501
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
CeleraX98,900,961 - 98,911,320 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006227440   ⟹   XP_006227502
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
CeleraX98,900,961 - 98,911,320 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006227441   ⟹   XP_006227503
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
CeleraX98,900,961 - 98,911,320 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006227442   ⟹   XP_006227504
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
CeleraX98,900,961 - 98,911,320 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006257237   ⟹   XP_006257299
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X97,860,526 - 97,870,912 (+)NCBI
Rnor_6.0X105,497,277 - 105,507,636 (+)NCBI
Rnor_5.0X105,386,682 - 105,396,989 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006257238   ⟹   XP_006257300
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X97,860,526 - 97,870,912 (+)NCBI
Rnor_6.0X105,497,277 - 105,507,636 (+)NCBI
Rnor_5.0X105,386,682 - 105,396,989 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006257239   ⟹   XP_006257301
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X97,860,526 - 97,870,912 (+)NCBI
Rnor_6.0X105,497,277 - 105,507,636 (+)NCBI
Rnor_5.0X105,386,682 - 105,396,989 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006257240   ⟹   XP_006257302
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0X105,497,277 - 105,507,636 (+)NCBI
Rnor_5.0X105,386,682 - 105,396,989 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006257241   ⟹   XP_006257303
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X97,860,526 - 97,870,912 (+)NCBI
Rnor_6.0X105,497,277 - 105,507,636 (+)NCBI
Rnor_5.0X105,386,682 - 105,396,989 (+)NCBI
Sequence:
RefSeq Acc Id: XM_008758501   ⟹   XP_008756723
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
CeleraX98,901,178 - 98,911,320 (+)NCBI
Sequence:
RefSeq Acc Id: XM_008758502   ⟹   XP_008756724
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
CeleraX98,900,961 - 98,911,320 (+)NCBI
Sequence:
RefSeq Acc Id: XM_008773454   ⟹   XP_008771676
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X97,860,786 - 97,870,912 (+)NCBI
Rnor_6.0X105,497,494 - 105,507,636 (+)NCBI
Sequence:
RefSeq Acc Id: XM_008773455   ⟹   XP_008771677
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0X105,497,277 - 105,507,636 (+)NCBI
Sequence:
RefSeq Acc Id: XM_039100645   ⟹   XP_038956573
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X97,860,786 - 97,870,912 (+)NCBI
Reference Sequences
RefSeq Acc Id: XP_006227501   ⟸   XM_006227439
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_006227500   ⟸   XM_006227438
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_006227503   ⟸   XM_006227441
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: XP_006227504   ⟸   XM_006227442
- Peptide Label: isoform X3
- Sequence:
RefSeq Acc Id: XP_006227502   ⟸   XM_006227440
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_006257300   ⟸   XM_006257238
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_006257299   ⟸   XM_006257237
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_006257302   ⟸   XM_006257240
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: XP_006257303   ⟸   XM_006257241
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: XP_006257301   ⟸   XM_006257239
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_008756724   ⟸   XM_008758502
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_008756723   ⟸   XM_008758501
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_008771677   ⟸   XM_008773455
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_008771676   ⟸   XM_008773454
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: ENSRNOP00000051224   ⟸   ENSRNOT00000040476
RefSeq Acc Id: XP_038956573   ⟸   XM_039100645
- Peptide Label: isoform X1
Protein Domains
Arm_2

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)
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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
SHRSP/Gcrc (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
SR/JrHsd (MCW)
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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)
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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
SS/Jr (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
SS/JrHsdMcwi (MCW)
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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)
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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
WAG/Rij (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/Gcrc (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/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
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
Damaging Variants


Assembly: Rnor_5.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
X 105392995 105392996 A G snv LEC/Tj (KyushuU)
X 105393163 105393164 C T snv MNS/Gib (KNAW)
X 105394864 105394865 C T snv LEC/Tj (KyushuU)
X 105395295 105395296 A G snv WAG/Rij (KNAW), NIG-III/Hok (KyushuU), RCS/Kyo (KyushuU), MR/N (KNAW), FHL/EurMcwi (MCW), GH/OmrMcwi (MCW), FHL/EurMcwi (KNAW)


Assembly: Rnor_6.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
X 105503810 105503811 C T snv MNS/Gib (RGD)
X 105505942 105505943 A G snv GH/OmrMcwi (MCW), FHL/EurMcwi (MCW), MR/N (MCW), WAG/Rij (RGD), FHL/EurMcwi (RGD)
X 105505975 105505976 T C snv WKY/N (MCW)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:2325053 AgrOrtholog
Ensembl Genes ENSRNOG00000043128 Ensembl, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000051224 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000040476 UniProtKB/TrEMBL
InterPro ARM-rpt_dom UniProtKB/TrEMBL
  ARM-type_fold UniProtKB/TrEMBL
  Armadillo UniProtKB/TrEMBL
NCBI Gene 100359678 ENTREZGENE
Pfam Arm_2 UniProtKB/TrEMBL
PhenoGen Armcx4 PhenoGen
PROSITE ARM_REPEAT UniProtKB/TrEMBL
Superfamily-SCOP SSF48371 UniProtKB/TrEMBL
UniProt D3ZV39_RAT UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2012-07-24 Armcx4  armadillo repeat containing, X-linked 4  LOC100359678  armadillo repeat containing, X-linked 4  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2010-05-20 LOC100359678  armadillo repeat containing, X-linked 4      Symbol and Name status set to provisional 70820 PROVISIONAL