Arvcf (ARVCF, delta catenin family member) - Rat Genome Database

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Gene: Arvcf (ARVCF, delta catenin family member) Rattus norvegicus
Analyze
Symbol: Arvcf
Name: ARVCF, delta catenin family member
RGD ID: 1306655
Description: Predicted to enable cadherin binding activity. Predicted to be involved in RNA splicing; cell-cell adhesion; and cell-cell junction assembly. Predicted to be part of messenger ribonucleoprotein complex. Predicted to be active in several cellular components, including adherens junction; nucleus; and plasma membrane. Human ortholog(s) of this gene implicated in DiGeorge syndrome. Orthologous to human ARVCF (ARVCF delta catenin family member); INTERACTS WITH acetamide; amphetamine; Cuprizon.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: armadillo repeat gene deleted in velo-cardio-facial syndrome; armadillo repeat protein deleted in velo-cardio-facial syndrome; armadillo repeat protein deleted in velo-cardio-facial syndrome homolog; LOC303798; MGC188400; similar to myosin heavy chain Myr 8; splicing regulator ARVCF
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
mRatBN7.21182,588,137 - 82,645,805 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1182,587,881 - 82,645,805 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1191,316,532 - 91,374,223 (-)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.01183,977,756 - 84,035,451 (-)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.01183,031,268 - 83,088,963 (-)NCBIRnor_WKY
Rnor_6.01186,736,125 - 86,793,795 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1186,736,142 - 86,793,791 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01189,830,063 - 89,887,729 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41184,582,208 - 84,639,874 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11184,622,916 - 84,680,863 (-)NCBI
Celera1181,365,200 - 81,422,823 (-)NCBICelera
Cytogenetic Map11q23NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component
adherens junction  (IBA,ISO,ISS)
anchoring junction  (IEA)
cytoplasm  (IBA,IEA,ISO,ISS)
messenger ribonucleoprotein complex  (ISO,ISS)
nucleus  (IBA,IEA,ISO,ISS)
plasma membrane  (IBA,IEA,ISO)

Molecular Function
cadherin binding  (IBA,ISO,ISS)
protein binding  (ISO)

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 GOA human gene data--August 2006 GOA data from the GO Consortium
3. The armadillo repeat region targets ARVCF to cadherin-based cellular junctions. Kaufmann U, etal., J Cell Sci. 2000 Nov;113 ( Pt 22):4121-35.
4. Association of ARVCF with zonula occludens (ZO)-1 and ZO-2: binding to PDZ-domain proteins and cell-cell adhesion regulate plasma membrane and nuclear localization of ARVCF. Kausalya PJ, etal., Mol Biol Cell. 2004 Dec;15(12):5503-15. Epub 2004 Sep 29.
5. The Erbin PDZ domain binds with high affinity and specificity to the carboxyl termini of delta-catenin and ARVCF. Laura RP, etal., J Biol Chem. 2002 Apr 12;277(15):12906-14. Epub 2002 Jan 30.
6. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
7. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
8. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
9. Identification of a new human catenin gene family member (ARVCF) from the region deleted in velo-cardio-facial syndrome. Sirotkin H, etal., Genomics. 1997 Apr 1;41(1):75-83.
Additional References at PubMed
PMID:11719554   PMID:12477932   PMID:22871113  


Genomics

Comparative Map Data
Arvcf
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21182,588,137 - 82,645,805 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1182,587,881 - 82,645,805 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1191,316,532 - 91,374,223 (-)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.01183,977,756 - 84,035,451 (-)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.01183,031,268 - 83,088,963 (-)NCBIRnor_WKY
Rnor_6.01186,736,125 - 86,793,795 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1186,736,142 - 86,793,791 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01189,830,063 - 89,887,729 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41184,582,208 - 84,639,874 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11184,622,916 - 84,680,863 (-)NCBI
Celera1181,365,200 - 81,422,823 (-)NCBICelera
Cytogenetic Map11q23NCBI
ARVCF
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh382219,965,134 - 20,016,823 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 Ensembl2219,969,896 - 20,016,823 (-)EnsemblGRCh38hg38GRCh38
GRCh372219,957,419 - 20,004,346 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 362218,337,419 - 18,384,309 (-)NCBINCBI36Build 36hg18NCBI36
Build 342218,331,972 - 18,378,863NCBI
Celera223,808,603 - 3,855,512 (-)NCBICelera
Cytogenetic Map22q11.21NCBI
HuRef223,577,880 - 3,624,971 (-)NCBIHuRef
CHM1_12219,957,112 - 20,004,018 (-)NCBICHM1_1
T2T-CHM13v2.02220,347,523 - 20,394,441 (-)NCBIT2T-CHM13v2.0
Arvcf
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391618,166,046 - 18,225,826 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1618,166,046 - 18,225,826 (+)EnsemblGRCm39 Ensembl
GRCm381618,348,182 - 18,407,076 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1618,348,182 - 18,407,076 (+)EnsemblGRCm38mm10GRCm38
MGSCv371618,348,367 - 18,407,169 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361618,261,837 - 18,320,639 (+)NCBIMGSCv36mm8
Celera1618,921,019 - 18,980,851 (+)NCBICelera
Cytogenetic Map16A3NCBI
cM Map1611.37NCBI
Arvcf
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495544218,109,439 - 18,127,971 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495544218,109,421 - 18,149,969 (+)NCBIChiLan1.0ChiLan1.0
ARVCF
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.12218,403,239 - 18,449,183 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl2218,403,239 - 18,449,183 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0222,729,706 - 2,779,034 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
ARVCF
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12629,304,710 - 29,359,110 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2629,307,351 - 29,359,245 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2629,262,926 - 29,317,272 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.02630,708,132 - 30,762,235 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl2630,710,265 - 30,762,237 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.12628,755,985 - 28,810,334 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.02628,381,348 - 28,435,692 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.02629,466,364 - 29,521,299 (+)NCBIUU_Cfam_GSD_1.0
Arvcf
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024405118138,819,333 - 138,869,607 (+)NCBIHiC_Itri_2
SpeTri2.0NW_0049366193,884,450 - 3,934,559 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
ARVCF
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1451,403,923 - 51,440,058 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11451,403,215 - 51,440,036 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21455,040,562 - 55,076,647 (-)NCBISscrofa10.2Sscrofa10.2susScr3
ARVCF
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1195,721,887 - 5,775,910 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl195,755,146 - 5,775,109 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_0236660851,156,666 - 1,210,971 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Arvcf
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_004624747591,891 - 610,988 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_004624747590,293 - 643,797 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
724554Iddm17Insulin dependent diabetes mellitus QTL 170.001blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)111897620886241447Rat
724563Uae10Urinary albumin excretion QTL 106urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)112767241082846715Rat
1581565Pur10Proteinuria QTL 100.0001urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)114480331882846466Rat
1581572Uae35Urinary albumin excretion QTL 350.0001urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)114480331882846466Rat
724561Plsm4Polydactyly-luxate syndrome (PLS) morphotypes QTL 40.0003forelimb integrity trait (VT:0010562)front foot phalanges count (CMO:0001947)115445753486241447Rat
4889521Gluco62Glucose level QTL 622.820.001blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)115513672982993457Rat
7411658Foco27Food consumption QTL 2716.20.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)115635142486241447Rat
10058954Gmadr7Adrenal mass QTL 72.490.0049adrenal gland mass (VT:0010420)both adrenal glands wet weight to body weight ratio (CMO:0002411)116034659086241447Rat
634339Niddm50Non-insulin dependent diabetes mellitus QTL 503.32blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)116642214886241447Rat
1354593Stl12Serum triglyceride level QTL 123.36blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)116642214886241447Rat
1354656Bvd3Brain ventricular dilatation QTL 33.640.001brain ventricle morphology trait (VT:0000822)hydrocephalus severity score (CMO:0001881)116944607082846715Rat
10450831Scl80Serum cholesterol level QTL 804.70.01blood LDL cholesterol amount (VT:0000181)blood low density lipoprotein cholesterol level (CMO:0000053)117695713183051965Rat
2302043Pia27Pristane induced arthritis QTL 2718.60.001blood immunoglobulin amount (VT:0002460)serum immunoglobulin M-type rheumatoid factor level relative to an arbitrary reference serum (CMO:0002111)118256654583440803Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:354
Count of miRNA genes:198
Interacting mature miRNAs:235
Transcripts:ENSRNOT00000044635
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 28 32 24 17 24 67 34 30 11
Low 3 15 25 17 2 17 8 11 7 1 11 8
Below cutoff

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_001131013 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006248617 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006248618 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008768880 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017597954 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017597955 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017597956 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017597957 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017597958 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017597959 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017597960 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017597961 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017597962 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AC121199 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC168253 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH473999 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JACYVU010000222 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000044635   ⟹   ENSRNOP00000047113
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1182,588,154 - 82,645,805 (-)Ensembl
Rnor_6.0 Ensembl1186,736,142 - 86,793,791 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000108636   ⟹   ENSRNOP00000076401
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1182,587,881 - 82,645,805 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000115091   ⟹   ENSRNOP00000092142
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1182,587,881 - 82,602,572 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000117187   ⟹   ENSRNOP00000079572
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1182,587,881 - 82,645,805 (-)Ensembl
RefSeq Acc Id: NM_001131013   ⟹   NP_001124485
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21182,588,137 - 82,645,805 (-)NCBI
Rnor_6.01186,736,125 - 86,793,791 (-)NCBI
Rnor_5.01189,830,063 - 89,887,729 (-)NCBI
RGSC_v3.41184,582,208 - 84,639,874 (-)RGD
Celera1181,365,200 - 81,422,823 (-)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_001124485 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAI68253 (Get FASTA)   NCBI Sequence Viewer  
  B4F7F3 (Get FASTA)   NCBI Sequence Viewer  
  EDL77939 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_001124485   ⟸   NM_001131013
- UniProtKB: B4F7F3 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000047113   ⟸   ENSRNOT00000044635
RefSeq Acc Id: ENSRNOP00000092142   ⟸   ENSRNOT00000115091
RefSeq Acc Id: ENSRNOP00000079572   ⟸   ENSRNOT00000117187
RefSeq Acc Id: ENSRNOP00000076401   ⟸   ENSRNOT00000108636

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-B4F7F3-F1-model_v2 AlphaFold B4F7F3 1-973 view protein structure

Transcriptome

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


Strain Variation

Strain Sequence Variants (mRatBN7.2)
ACI/EurMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
ACI/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN-Lx/CubMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BUF/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH2/CubMcwi (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH3/CubMcwi (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
DA/OlaHsd (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/DuCrl (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/NCrl (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/Stm (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FHH/EurMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FXLE16/Stm (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FXLE18/Stm (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
GK/FarMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB10/IpcvMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB2/IpcvMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB20/IpcvMcwi (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB31/IpcvMcwi (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB4/IpcvMcwi (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEW/Crl (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF10A/StmMcwi (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF11/Stm (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1A/Stm (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1C/Stm (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF2B/Stm (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF3/Stm (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF4/Stm (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LH/MavRrrcAek (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LL/MavRrrcAek (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LN/MavRrrcAek (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/N (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/NRrrcMcwi (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MR/N (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MWF/Hsd (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
PVG/Seac (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHR/OlalpcvMcwi (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/A3NCrl (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SR/JrHsd (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SS/JrHsdMcwi (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WAG/RijCrl (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/N (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/NCrl (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WN/N (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
Damaging Variants


Assembly: Rnor_6.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
11 86736847 86736848 A G snv CDR, GH/OmrMcwi (MCW), WN/N (2020), MWF/Hsd (2019), WN/N (MCW)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1306655 AgrOrtholog
BioCyc Gene G2FUF-20659 BioCyc
Ensembl Genes ENSRNOG00000001888 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000047113 ENTREZGENE
  ENSRNOP00000047113.4 UniProtKB/TrEMBL
  ENSRNOP00000076401.1 UniProtKB/TrEMBL
  ENSRNOP00000079572.1 UniProtKB/TrEMBL
  ENSRNOP00000092142.1 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000044635 ENTREZGENE
  ENSRNOT00000044635.6 UniProtKB/TrEMBL
  ENSRNOT00000108636.1 UniProtKB/TrEMBL
  ENSRNOT00000115091.1 UniProtKB/TrEMBL
  ENSRNOT00000117187.1 UniProtKB/TrEMBL
Gene3D-CATH 1.25.10.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
InterPro ARM-like UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  ARM-type_fold UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Armadillo UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  ARVCF UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Plakophilin/d_Catenin UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:303798 UniProtKB/Swiss-Prot
NCBI Gene 303798 ENTREZGENE
PANTHER PTHR10372 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PTHR10372:SF5 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam Arm UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Arvcf PhenoGen
PROSITE ARM_REPEAT UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART ARM UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP ARM-type_fold UniProtKB/TrEMBL, UniProtKB/Swiss-Prot
UniProt A0A8I5Y059_RAT UniProtKB/TrEMBL
  A0A8I5ZNA5_RAT UniProtKB/TrEMBL
  A0A8I6ADG5_RAT UniProtKB/TrEMBL
  ARVC_RAT UniProtKB/Swiss-Prot, ENTREZGENE
  F7FK74_RAT UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2017-08-18 Arvcf  ARVCF, delta catenin family member  Arvcf  armadillo repeat gene deleted in velo-cardio-facial syndrome  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2013-05-24 Arvcf  armadillo repeat gene deleted in velo-cardio-facial syndrome  LOC680480  similar to myosin heavy chain Myr 8  Data Merged 1643240 APPROVED
2013-05-24 Arvcf  armadillo repeat gene deleted in velo-cardio-facial syndrome  LOC682600  similar to myosin heavy chain Myr 8  Data Merged 1643240 APPROVED
2008-04-30 Arvcf  armadillo repeat gene deleted in velo-cardio-facial syndrome   Arvcf_predicted  armadillo repeat gene deleted in velo-cardio-facial syndrome (predicted)  'predicted' is removed 2292626 APPROVED
2006-11-20 LOC682600  similar to myosin heavy chain Myr 8      Symbol and Name status set to provisional 70820 PROVISIONAL
2006-11-20 LOC680480  similar to myosin heavy chain Myr 8      Symbol and Name status set to provisional 70820 PROVISIONAL
2005-01-12 Arvcf_predicted  armadillo repeat gene deleted in velo-cardio-facial syndrome (predicted)      Symbol and Name status set to approved 70820 APPROVED