Xirp1 (xin actin-binding repeat containing 1) - Rat Genome Database
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Gene: Xirp1 (xin actin-binding repeat containing 1) Rattus norvegicus
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Symbol: Xirp1
Name: xin actin-binding repeat containing 1
RGD ID: 1304776
Description: Predicted to have actin filament binding activity. Predicted to be involved in several processes, including Notch signaling pathway; negative regulation of protein binding activity; and striated muscle cell development. Predicted to colocalize with focal adhesion and stress fiber. Orthologous to human XIRP1 (xin actin binding repeat containing 1); INTERACTS WITH 1,3-dinitrobenzene; 2,3,7,8-Tetrachlorodibenzofuran; 6-propyl-2-thiouracil.
Type: protein-coding
RefSeq Status: MODEL
Also known as: cardiomyopathy associated 1; Cmya1; LOC100910104; LOC316071; xin actin-binding repeat-containing protein 1; xin actin-binding repeat-containing protein 1-like
Orthologs:
Homo sapiens (human) : XIRP1 (xin actin binding repeat containing 1)  HGNC  Alliance
Mus musculus (house mouse) : Xirp1 (xin actin-binding repeat containing 1)  MGI  Alliance
Chinchilla lanigera (long-tailed chinchilla) : Xirp1 (xin actin binding repeat containing 1)
Pan paniscus (bonobo/pygmy chimpanzee) : XIRP1 (xin actin binding repeat containing 1)
Canis lupus familiaris (dog) : XIRP1 (xin actin binding repeat containing 1)
Ictidomys tridecemlineatus (thirteen-lined ground squirrel) : Xirp1 (xin actin binding repeat containing 1)
Sus scrofa (pig) : XIRP1 (xin actin binding repeat containing 1)
Chlorocebus sabaeus (African green monkey) : XIRP1 (xin actin binding repeat containing 1)
Heterocephalus glaber (naked mole-rat) : Xirp1 (xin actin binding repeat containing 1)
more info ...
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rnor_6.08128,694,809 - 128,712,092 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl8128,702,133 - 128,711,221 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.08127,903,077 - 127,912,966 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.48124,995,308 - 125,001,397 (-)NCBIRGSC3.4rn4RGSC3.4
Celera8118,886,557 - 118,903,852 (-)NCBICelera
Cytogenetic Map8q32NCBI
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

Molecular Function

References

Additional References at PubMed
PMID:10021346   PMID:12203715   PMID:15454575   PMID:16708114   PMID:17766470   PMID:17855775   PMID:22658674   PMID:23117660  


Genomics

Comparative Map Data
Xirp1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rnor_6.08128,694,809 - 128,712,092 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl8128,702,133 - 128,711,221 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.08127,903,077 - 127,912,966 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.48124,995,308 - 125,001,397 (-)NCBIRGSC3.4rn4RGSC3.4
Celera8118,886,557 - 118,903,852 (-)NCBICelera
Cytogenetic Map8q32NCBI
XIRP1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl339,183,210 - 39,192,596 (-)EnsemblGRCh38hg38GRCh38
GRCh38339,183,214 - 39,192,621 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh37339,224,706 - 39,234,112 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36339,199,711 - 39,209,081 (-)NCBINCBI36hg18NCBI36
Celera339,166,370 - 39,175,740 (-)NCBI
Cytogenetic Map3p22.2NCBI
HuRef339,267,117 - 39,276,496 (-)NCBIHuRef
CHM1_1339,175,713 - 39,185,094 (-)NCBICHM1_1
Xirp1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm399119,842,821 - 119,852,664 (-)NCBI
GRCm389120,013,755 - 120,023,598 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl9120,013,755 - 120,023,598 (-)EnsemblGRCm38mm10GRCm38
MGSCv379119,922,873 - 119,932,716 (-)NCBIGRCm37mm9NCBIm37
MGSCv369119,862,453 - 119,872,296 (-)NCBImm8
Celera9120,481,114 - 120,490,957 (-)NCBICelera
Cytogenetic Map9F4NCBI
Xirp1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495542724,781,194 - 24,786,728 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495542724,778,157 - 24,787,691 (+)NCBIChiLan1.0ChiLan1.0
XIRP1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1339,360,422 - 39,369,807 (-)NCBIpanpan1.1PanPan1.1panPan2
Mhudiblu_PPA_v0339,079,712 - 39,089,098 (-)NCBIMhudiblu_PPA_v0panPan3
XIRP1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1 Ensembl238,851,832 - 8,855,862 (-)EnsemblCanFam3.1canFam3CanFam3.1
CanFam3.1238,849,713 - 8,859,515 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Xirp1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
SpeTri2.0NW_00493647328,434,910 - 28,444,146 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
XIRP1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1323,867,478 - 23,873,589 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11323,867,476 - 23,876,850 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21326,127,756 - 26,137,310 (-)NCBISscrofa10.2Sscrofa10.2susScr3
XIRP1
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.115221,365 - 232,284 (+)NCBI
Xirp1
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046247311,779,004 - 1,788,668 (+)NCBI

Position Markers
RH132161  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.08128,702,297 - 128,702,479NCBIRnor6.0
Rnor_5.08127,903,194 - 127,903,376UniSTSRnor5.0
RGSC_v3.48124,995,425 - 124,995,607UniSTSRGSC3.4
Celera8118,894,057 - 118,894,239UniSTS
Cytogenetic Map8q32UniSTS
RH 3.4 Map81286.5UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
2300181Bmd55Bone mineral density QTL 555.70.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)883894304128894304Rat
61437Cia6Collagen induced arthritis QTL 6joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)889058229132243842Rat
1358893Bp263Blood pressure QTL 2635.01arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)8100873811133307652Rat
1358903Bp252Blood pressure QTL 25270.0001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)8100873811133307652Rat
738011Anxrr9Anxiety related response QTL 96.1exploratory behavior trait (VT:0010471)number of entries into a discrete space in an experimental apparatus (CMO:0000960)8102051964133307652Rat
738014Anxrr15Anxiety related response QTL 153.60.005locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)8104682575133307652Rat
2300182Bmd56Bone mineral density QTL 565.4femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)8104682575133307652Rat
724539Cm19Cardiac mass QTL 192.6heart mass (VT:0007028)calculated heart weight (CMO:0000073)8107769005129956433Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:76
Count of miRNA genes:63
Interacting mature miRNAs:65
Transcripts:ENSRNOT00000055888
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.


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 43 8 11 7 1 8
Low 8 6 2 6 4 7 7
Below cutoff 2 25 11 16 11 48 33 27 3

Sequence

Nucleotide Sequences
RefSeq Transcripts XM_006226620 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006226624 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006244151 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006244155 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008757884 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008766701 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017596154 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017603735 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XR_001839577 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XR_001839578 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XR_001839579 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XR_001844797 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XR_001844798 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XR_001844799 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AABR07071742 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AAHX01057553 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000055888   ⟹   ENSRNOP00000052739
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl8128,702,133 - 128,711,221 (-)Ensembl
RefSeq Acc Id: XM_006226620   ⟹   XP_006226682
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Celera8118,893,940 - 118,903,829 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006226624   ⟹   XP_006226686
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Celera8118,896,141 - 118,903,829 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006244151   ⟹   XP_006244213
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.08128,702,180 - 128,712,069 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006244155   ⟹   XP_006244217
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.08128,704,381 - 128,712,069 (-)NCBI
Sequence:
RefSeq Acc Id: XM_008757884   ⟹   XP_008756106
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Celera8118,893,940 - 118,903,830 (-)NCBI
Sequence:
RefSeq Acc Id: XM_008766701   ⟹   XP_008764923
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.08128,702,180 - 128,712,070 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017596154   ⟹   XP_017451643
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.08128,702,180 - 128,710,694 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017603735   ⟹   XP_017459224
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Celera8118,893,940 - 118,902,454 (-)NCBI
Sequence:
RefSeq Acc Id: XR_001839577
RefSeq Status:
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.08128,699,491 - 128,712,083 (-)NCBI
Sequence:
RefSeq Acc Id: XR_001839578
RefSeq Status:
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.08128,694,809 - 128,712,092 (-)NCBI
Sequence:
RefSeq Acc Id: XR_001839579
RefSeq Status:
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.08128,699,491 - 128,712,092 (-)NCBI
Sequence:
RefSeq Acc Id: XR_001844797
RefSeq Status:
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
Celera8118,891,251 - 118,903,843 (-)NCBI
Sequence:
RefSeq Acc Id: XR_001844798
RefSeq Status:
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
Celera8118,886,557 - 118,903,852 (-)NCBI
Sequence:
RefSeq Acc Id: XR_001844799
RefSeq Status:
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
Celera8118,891,251 - 118,903,852 (-)NCBI
Sequence:
Reference Sequences
RefSeq Acc Id: XP_008756106   ⟸   XM_008757884
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_006226682   ⟸   XM_006226620
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_006226686   ⟸   XM_006226624
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: XP_008764923   ⟸   XM_008766701
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_006244213   ⟸   XM_006244151
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_006244217   ⟸   XM_006244155
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: XP_017459224   ⟸   XM_017603735
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_017451643   ⟸   XM_017596154
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: ENSRNOP00000052739   ⟸   ENSRNOT00000055888

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)
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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: SBH/Ygl sequenced by MCW
SBH/Ygl (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
SBN/Ygl (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: SBN/Ygl sequenced by MCW
SBN/Ygl (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
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

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1304776 AgrOrtholog
Ensembl Genes ENSRNOG00000037085 Ensembl, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000052739 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000055888 UniProtKB/TrEMBL
InterPro Actin-binding_Xin_repeat UniProtKB/TrEMBL
  XIRP1/XIRP2 UniProtKB/TrEMBL
NCBI Gene Xirp1 ENTREZGENE
PANTHER PTHR22591 UniProtKB/TrEMBL
Pfam Xin UniProtKB/TrEMBL
PhenoGen Xirp1 PhenoGen
PROSITE XIN UniProtKB/TrEMBL
UniProt D4ABA9_RAT UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2015-03-16 Xirp1  xin actin-binding repeat containing 1  Xirp1  xin actin-binding repeat containing 1  Type changed (type changed from [null] to [protein-coding]) 629549 APPROVED
2015-02-26 Xirp1  xin actin-binding repeat containing 1  LOC100910104  xin actin-binding repeat-containing protein 1-like  Data Merged 737654 APPROVED
2012-07-05 LOC100910104  xin actin-binding repeat-containing protein 1-like      Symbol and Name status set to provisional 70820 PROVISIONAL
2008-03-03 Xirp1  xin actin-binding repeat containing 1  Cmya1_predicted  cardiomyopathy associated 1 (predicted)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2005-01-12 Cmya1_predicted  cardiomyopathy associated 1 (predicted)      Symbol and Name status set to approved 70820 APPROVED