Xirp1 (xin actin-binding repeat containing 1) - Rat Genome Database

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Gene: Xirp1 (xin actin-binding repeat containing 1) Rattus norvegicus
Analyze
Symbol: Xirp1
Name: xin actin-binding repeat containing 1
RGD ID: 1304776
Description: Predicted to enable actin filament binding activity. Predicted to be involved in actin filament organization. Predicted to act upstream of or within several processes, including Notch signaling pathway; muscle cell development; and negative regulation of cell population proliferation. Predicted to be located in adherens junction and fascia adherens. 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-tetrachlorodibenzodioxine; 2,3,7,8-Tetrachlorodibenzofuran.
Type: protein-coding
RefSeq Status: MODEL
Previously known as: cardiomyopathy associated 1; Cmya1; LOC100910104; LOC316071; xin actin-binding repeat-containing protein 1; xin actin-binding repeat-containing protein 1-like
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr88128,625,111 - 128,635,011 (-)NCBIGRCr8
mRatBN7.28119,744,778 - 119,757,547 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl8119,747,419 - 119,757,349 (-)EnsemblmRatBN7.2 Ensembl
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 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
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

References - curated
# Reference Title Reference Citation
1. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
2. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
3. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
4. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:10021346   PMID:12203715   PMID:15454575   PMID:16708114   PMID:17766470   PMID:17855775   PMID:22658674   PMID:23117660   PMID:33261556   PMID:35352799  


Genomics

Comparative Map Data
Xirp1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr88128,625,111 - 128,635,011 (-)NCBIGRCr8
mRatBN7.28119,744,778 - 119,757,547 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl8119,747,419 - 119,757,349 (-)EnsemblmRatBN7.2 Ensembl
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 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera8118,886,557 - 118,903,852 (-)NCBICelera
Cytogenetic Map8q32NCBI
XIRP1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38339,183,215 - 39,192,595 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl339,183,210 - 39,192,596 (-)EnsemblGRCh38hg38GRCh38
GRCh37339,224,706 - 39,234,086 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36339,199,711 - 39,209,081 (-)NCBINCBI36Build 36hg18NCBI36
Celera339,166,370 - 39,175,740 (-)NCBICelera
Cytogenetic Map3p22.2NCBI
HuRef339,267,117 - 39,276,496 (-)NCBIHuRef
CHM1_1339,175,713 - 39,185,092 (-)NCBICHM1_1
T2T-CHM13v2.0339,196,207 - 39,205,587 (-)NCBIT2T-CHM13v2.0
Xirp1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm399119,842,821 - 119,852,660 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl9119,842,821 - 119,852,664 (-)EnsemblGRCm39 Ensembl
GRCm389120,013,755 - 120,023,598 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl9120,013,755 - 120,023,598 (-)EnsemblGRCm38mm10GRCm38
MGSCv379119,922,873 - 119,932,716 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv369119,862,453 - 119,872,296 (-)NCBIMGSCv36mm8
Celera9120,481,114 - 120,490,957 (-)NCBICelera
Cytogenetic Map9F4NCBI
cM Map971.36NCBI
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
NHGRI_mPanPan1-v2239,135,077 - 39,144,458 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1339,139,839 - 39,149,220 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0339,079,712 - 39,089,098 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1339,360,422 - 39,369,807 (-)NCBIpanpan1.1PanPan1.1panPan2
XIRP1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1238,849,713 - 8,859,515 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl238,851,832 - 8,855,862 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha238,885,546 - 8,895,280 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0239,134,253 - 9,144,014 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl239,134,262 - 9,144,031 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1238,947,857 - 8,957,600 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0239,090,432 - 9,096,578 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0239,083,694 - 9,093,470 (-)NCBIUU_Cfam_GSD_1.0
Xirp1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024405118195,296,276 - 195,305,601 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_00493647328,436,996 - 28,444,176 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_00493647328,434,910 - 28,444,146 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
XIRP1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1323,867,474 - 23,876,852 (-)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 - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.115221,365 - 232,284 (+)NCBIChlSab1.1ChlSab1.1chlSab2
Vero_WHO_p1.0NW_0236660638,950,122 - 8,956,678 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Xirp1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046247311,782,128 - 1,787,647 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046247311,779,004 - 1,788,668 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Xirp1
25 total Variants
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.


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1554321Bmd3Bone mineral density QTL 37.90.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)840952565123900184Rat
2300181Bmd55Bone mineral density QTL 555.70.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)876468691121468691Rat
61437Cia6Collagen induced arthritis QTL 6joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)882460758122812818Rat
738011Anxrr9Anxiety related response QTL 96.1exploratory behavior trait (VT:0010471)number of entries into a discrete space in an experimental apparatus (CMO:0000960)893535351123900184Rat
1358893Bp263Blood pressure QTL 2635.01arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)893965141123900184Rat
1358903Bp252Blood pressure QTL 25270.0001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)893965141123900184Rat
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)895718998123900184Rat
2300182Bmd56Bone mineral density QTL 565.4femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)895718998123900184Rat
724539Cm19Cardiac mass QTL 192.6heart mass (VT:0007028)calculated heart weight (CMO:0000073)8100149864120994388Rat

Markers in Region
RH132161  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.28119,747,583 - 119,747,766 (+)MAPPERmRatBN7.2
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
RH 3.4 Map81286.5UniSTS
Cytogenetic Map8q32UniSTS


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
  XM_039082728 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_063266351 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_063266352 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XR_001839578 (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 JAXUCZ010000008 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000055888   ⟹   ENSRNOP00000052739
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl8119,747,456 - 119,757,349 (-)Ensembl
Rnor_6.0 Ensembl8128,702,133 - 128,711,221 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000093872   ⟹   ENSRNOP00000077004
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl8119,747,419 - 119,756,246 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000101246   ⟹   ENSRNOP00000091019
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl8119,747,422 - 119,757,337 (-)Ensembl
RefSeq Acc Id: XM_006244151   ⟹   XP_006244213
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr88128,625,111 - 128,635,011 (-)NCBI
mRatBN7.28119,747,467 - 119,757,366 (-)NCBI
Rnor_6.08128,702,180 - 128,712,069 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006244155   ⟹   XP_006244217
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr88128,625,111 - 128,635,011 (-)NCBI
mRatBN7.28119,749,651 - 119,757,366 (-)NCBI
Rnor_6.08128,704,381 - 128,712,069 (-)NCBI
Sequence:
RefSeq Acc Id: XM_008766701   ⟹   XP_008764923
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr88128,625,111 - 128,635,003 (-)NCBI
mRatBN7.28119,747,467 - 119,757,366 (-)NCBI
Rnor_6.08128,702,180 - 128,712,070 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017596154   ⟹   XP_017451643
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr88128,625,111 - 128,633,154 (-)NCBI
mRatBN7.28119,747,467 - 119,756,027 (-)NCBI
Rnor_6.08128,702,180 - 128,710,694 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039082728   ⟹   XP_038938656
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr88128,625,111 - 128,633,152 (-)NCBI
mRatBN7.28119,747,467 - 119,756,027 (-)NCBI
RefSeq Acc Id: XM_063266351   ⟹   XP_063122421
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr88128,625,111 - 128,633,154 (-)NCBI
RefSeq Acc Id: XM_063266352   ⟹   XP_063122422
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr88128,625,111 - 128,633,152 (-)NCBI
Reference Protein Sequences
RefSeq Acc Id: XP_008764923   ⟸   XM_008766701
- Peptide Label: isoform X1
- UniProtKB: A0A8I5YBK9 (UniProtKB/TrEMBL),   A6I3Y7 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006244213   ⟸   XM_006244151
- Peptide Label: isoform X1
- UniProtKB: A0A8I5YBK9 (UniProtKB/TrEMBL),   A6I3Y7 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006244217   ⟸   XM_006244155
- Peptide Label: isoform X2
- UniProtKB: D4ABA9 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_017451643   ⟸   XM_017596154
- Peptide Label: isoform X1
- UniProtKB: A0A8I5YBK9 (UniProtKB/TrEMBL),   A6I3Y7 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000052739   ⟸   ENSRNOT00000055888
RefSeq Acc Id: XP_038938656   ⟸   XM_039082728
- Peptide Label: isoform X1
- UniProtKB: A0A8I5YBK9 (UniProtKB/TrEMBL),   A6I3Y7 (UniProtKB/TrEMBL)
RefSeq Acc Id: ENSRNOP00000077004   ⟸   ENSRNOT00000093872
RefSeq Acc Id: ENSRNOP00000091019   ⟸   ENSRNOT00000101246
RefSeq Acc Id: XP_063122421   ⟸   XM_063266351
- Peptide Label: isoform X2
- UniProtKB: D4ABA9 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_063122422   ⟸   XM_063266352
- Peptide Label: isoform X2
- UniProtKB: D4ABA9 (UniProtKB/TrEMBL)

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D4ABA9-F1-model_v2 AlphaFold D4ABA9 1-1153 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:1304776 AgrOrtholog
BioCyc Gene G2FUF-28769 BioCyc
Ensembl Genes ENSRNOG00000037085 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000055888.4 UniProtKB/TrEMBL
  ENSRNOT00000093872.1 UniProtKB/TrEMBL
  ENSRNOT00000101246.1 UniProtKB/TrEMBL
InterPro Actin-binding_Xin_repeat UniProtKB/TrEMBL
  XIRP1/XIRP2 UniProtKB/TrEMBL
KEGG Report rno:100910104 UniProtKB/TrEMBL
NCBI Gene Xirp1 ENTREZGENE
PANTHER PTHR22591 UniProtKB/TrEMBL
  XIN ACTIN-BINDING REPEAT-CONTAINING PROTEIN 1 UniProtKB/TrEMBL
Pfam Xin UniProtKB/TrEMBL
PhenoGen Xirp1 PhenoGen
PROSITE XIN UniProtKB/TrEMBL
RatGTEx ENSRNOG00000037085 RatGTEx
UniProt A0A8I5YBK9 ENTREZGENE, UniProtKB/TrEMBL
  A6I3Y7 ENTREZGENE, UniProtKB/TrEMBL
  D4ABA9 ENTREZGENE, 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 from RGD:6500102 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