Clca4c-ps (chloride channel accessory 4C, pseudogene) - Rat Genome Database

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Gene: Clca4c-ps (chloride channel accessory 4C, pseudogene) Mus musculus
Analyze
Symbol: Clca4c-ps
Name: chloride channel accessory 4C, pseudogene
RGD ID: 1617858
MGI Page MGI
Description: INTERACTS WITH triptonide; benzo[a]pyrene (ortholog); fenfluramine (ortholog)
Type: pseudo (Ensembl: lncRNA)
RefSeq Status: VALIDATED
Previously known as: Clca; Clca4c; EG622139; Gm18718; Gm6289; hypothetical protein LOC622139; predicted gene, 18718; uncharacterized protein LOC622139
RGD Orthologs
Human
Alliance Genes
More Info more info ...
Related Functional Gene: Clca4a  
Latest Assembly: GRCm39 - Mouse Genome Assembly GRCm39
Position:
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm393144,585,083 - 144,601,772 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl3144,567,587 - 144,595,506 (-)EnsemblGRCm39 Ensembl
GRCm39 Ensembl3144,585,083 - 144,601,772 (-)EnsemblGRCm39 Ensembl
GRCm383144,879,322 - 144,896,011 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl3144,861,826 - 144,896,011 (-)EnsemblGRCm38mm10GRCm38
MGSCv373144,542,289 - 144,558,975 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv363144,816,711 - 144,833,397 (-)NCBIMGSCv36mm8
Celera3151,320,459 - 151,337,145 (-)NCBICelera
Cytogenetic Map3H2NCBI
cM Map369.18NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
References

References - curated
# Reference Title Reference Citation
1. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:10349636   PMID:11042159   PMID:11076861   PMID:11217851   PMID:12466851   PMID:16141072   PMID:16141073  


Genomics

Comparative Map Data
Clca4c-ps
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm393144,585,083 - 144,601,772 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl3144,567,587 - 144,595,506 (-)EnsemblGRCm39 Ensembl
GRCm39 Ensembl3144,585,083 - 144,601,772 (-)EnsemblGRCm39 Ensembl
GRCm383144,879,322 - 144,896,011 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl3144,861,826 - 144,896,011 (-)EnsemblGRCm38mm10GRCm38
MGSCv373144,542,289 - 144,558,975 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv363144,816,711 - 144,833,397 (-)NCBIMGSCv36mm8
Celera3151,320,459 - 151,337,145 (-)NCBICelera
Cytogenetic Map3H2NCBI
cM Map369.18NCBI
CLCA3P
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38186,634,276 - 86,655,376 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl186,634,276 - 86,654,745 (+)EnsemblGRCh38hg38GRCh38
GRCh38.p14 Ensembl186,634,273 - 86,655,376 (+)EnsemblGRCh38hg38GRCh38
GRCh37187,099,959 - 87,121,059 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36186,872,547 - 86,893,647 (+)NCBINCBI36Build 36hg18NCBI36
Build 34186,811,979 - 86,833,080NCBI
Celera185,343,591 - 85,364,697 (+)NCBICelera
Cytogenetic Map1p22.3NCBI
HuRef185,210,349 - 85,231,447 (+)NCBIHuRef
CHM1_1187,214,797 - 87,235,895 (+)NCBICHM1_1
T2T-CHM13v2.0186,474,301 - 86,495,405 (+)NCBIT2T-CHM13v2.0

Variants

.
Variants in Clca4c-ps
715 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:60
Count of miRNA genes:52
Interacting mature miRNAs:53
Transcripts:ENSMUST00000098551, ENSMUST00000171492
Prediction methods:Miranda, Rnahybrid
Result types:miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.


QTLs in Region (GRCm39)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1302056Orgwq4_morgan weight QTL 4 (mouse)Not determined330067588147304689Mouse
27226732Tibmd3_mtibia midshaft diameter 3, 10 week (mouse)396607316147805636Mouse
1300752Ap6q_malcohol preference 6 QTL (mouse)Not determined3100372912147045722Mouse
27226733Tibmd6_mtibia midshaft diameter 6, 16 week (mouse)3101307316149805637Mouse
1302093Orgwq5_morgan weight QTL 5 (mouse)Not determined3107376936147304689Mouse
1301381Bomb1_mbone marrow pre-B 1 (mouse)Not determined3111133243145133417Mouse
1301100Bdt2_mbone density traits 2 (mouse)Not determined3114736617148736784Mouse
10043919Afpq8_mabdominal fat percent QTL 8 (mouse)Not determined3119057332153057456Mouse
1558868Ses9_msalmonella enteritidis susceptibility 9 (mouse)Not determined3119057332153057456Mouse
4141935Tgq15_mtriglyceride QTL 15 (mouse)Not determined119318586153318586Mouse
4142449Tgq14_mtriglyceride QTL 14 (mouse)Not determined119318586153318586Mouse
1302151Lprm2_mlymphoproliferation modifier 2 (mouse)Not determined3119778857153779044Mouse
10412240Alpq6_malcohol preference QTL 6 (mouse)Not determined3120772078154772078Mouse
4142245Pstc1_mperiosteal circumference 1 (mouse)Not determined3126270248159745316Mouse
1301218Letohc1_mlow ethanol consumption 1 (mouse)Not determined3126352986159745316Mouse
1301347Fpli_mfasting plasma insulin (mouse)Not determined3126460514159745316Mouse
1301563Alcp3_malcohol preference locus 3 (mouse)Not determined3130736935159745316Mouse
11039523Tbbr1_mTrypanosoma brucei brucei response 1 (mouse)3130849375159745316Mouse
1300753Eae10_msusceptibility to experimental allergic encephalomyelitis 10 (mouse)Not determined3131736617148451178Mouse
10412120Ccs3_mcolon cancer susceptibility 3 (mouse)Not determined3131754536146017669Mouse
1301528Loco1_mlocomotor activity 1 (mouse)Not determined3133461893159745316Mouse
1301221Hrtfm2_mheart failure modifier 2 (mouse)Not determined3143270248147045722Mouse
1301222Scc7_mcolon tumor susceptibility 7 (mouse)Not determined3143352986156364108Mouse

Markers in Region
AI504701  
Mouse AssemblyChrPosition (strand)SourceJBrowse
GRCm383144,952,690 - 144,952,831UniSTSGRCm38
GRCm383144,861,841 - 144,861,982UniSTSGRCm38
MGSCv373144,524,805 - 144,524,946UniSTSGRCm37
MGSCv373144,615,654 - 144,615,795UniSTSGRCm37
Celera3151,393,812 - 151,393,953UniSTS
Celera3151,302,797 - 151,302,938UniSTS
Cytogenetic Map3H2UniSTS
Whitehead/MRC_RH31594.43UniSTS


Expression


Sequence


Reference Sequences
RefSeq Acc Id: ENSMUST00000098551
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl3144,585,083 - 144,601,772 (-)Ensembl
GRCm38.p6 Ensembl3144,879,322 - 144,896,011 (-)Ensembl
RefSeq Acc Id: ENSMUST00000200595
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl3144,567,587 - 144,595,506 (-)Ensembl
GRCm38.p6 Ensembl3144,861,826 - 144,889,745 (-)Ensembl
RefSeq Acc Id: NR_126537
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm393144,585,083 - 144,601,772 (-)NCBI
GRCm383144,879,322 - 144,896,011 (-)NCBI
Celera3151,320,456 - 151,337,145 (-)NCBI
Sequence:
Protein Sequences
GenBank Protein BAE23897 (Get FASTA)   NCBI Sequence Viewer  
Reference Protein Sequences
Protein Domains
Calcium-activated chloride channel N-terminal


Additional Information

Database Acc Id Source(s)
AGR Gene MGI:3643218 AgrOrtholog
Ensembl Genes ENSMUSG00000074196 Ensembl
  ENSMUSG00000121400 Ensembl, ENTREZGENE
Ensembl Transcript ENSMUST00000098551 ENTREZGENE
InterPro Cl_channel_Ca UniProtKB/TrEMBL
MGD MGI:3643218 ENTREZGENE
NCBI Gene 622139 ENTREZGENE
Pfam CLCA_N UniProtKB/TrEMBL
PhenoGen Clca4c-ps PhenoGen
UniProt Q3UTT3_MOUSE UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-03-24 Clca4c-ps  chloride channel accessory 4C, pseudogene  Gm18718  predicted gene, 18718  Data merged from RGD:5142845 737654 PROVISIONAL
2015-10-20 Clca4c-ps  chloride channel accessory 4C, pseudogene    chloride channel calcium activated 4C, pseudogene  Symbol and/or name change 5135510 APPROVED
2015-01-27 Clca4c-ps  chloride channel calcium activated 4C, pseudogene  Clca4c  chloride channel calcium activated 4C  Symbol and/or name change 5135510 APPROVED
2014-11-26 Clca4c  chloride channel calcium activated 4C  Gm6289  predicted gene 6289  Symbol and/or name change 5135510 APPROVED