Pcid2 (PCI domain containing 2) - Rat Genome Database

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Gene: Pcid2 (PCI domain containing 2) Rattus norvegicus
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Symbol: Pcid2
Name: PCI domain containing 2
RGD ID: 1307041
Description: Predicted to enable RNA binding activity and double-stranded DNA binding activity. Predicted to be involved in several processes, including gene expression; post-transcriptional tethering of RNA polymerase II gene DNA at nuclear periphery; and regulation of RNA metabolic process. Predicted to be located in cytoplasm and nucleus. Predicted to be part of nuclear pore nuclear basket and transcription export complex 2. Orthologous to human PCID2 (PCI domain containing 2); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; bisphenol A; hexane.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: hypothetical protein LOC361182; LOC361182; PCI domain-containing protein 2; RGD1307041; similar to hypothetical protein FLJ11305; uncharacterized protein LOC361182
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
mRatBN7.21676,423,245 - 76,448,712 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1676,423,245 - 76,448,712 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1681,703,795 - 81,729,260 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01685,156,372 - 85,181,837 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01680,405,044 - 80,431,334 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01681,757,582 - 81,783,047 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1681,756,971 - 81,783,047 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01681,242,949 - 81,268,414 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41681,280,427 - 81,305,892 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11681,279,932 - 81,305,288 (+)NCBI
Celera1674,229,279 - 74,254,744 (+)NCBICelera
Cytogenetic Map16q12.5NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

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. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:12477932   PMID:20870947   PMID:23591820  


Genomics

Comparative Map Data
Pcid2
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21676,423,245 - 76,448,712 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1676,423,245 - 76,448,712 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1681,703,795 - 81,729,260 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01685,156,372 - 85,181,837 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01680,405,044 - 80,431,334 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01681,757,582 - 81,783,047 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1681,756,971 - 81,783,047 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01681,242,949 - 81,268,414 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41681,280,427 - 81,305,892 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11681,279,932 - 81,305,288 (+)NCBI
Celera1674,229,279 - 74,254,744 (+)NCBICelera
Cytogenetic Map16q12.5NCBI
PCID2
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh3813113,165,002 - 113,208,669 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl13113,177,536 - 113,208,715 (-)EnsemblGRCh38hg38GRCh38
GRCh3713113,831,850 - 113,862,983 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 3613112,879,927 - 112,910,984 (-)NCBINCBI36Build 36hg18NCBI36
Celera1394,658,168 - 94,689,275 (-)NCBICelera
Cytogenetic Map13q34NCBI
HuRef1394,270,740 - 94,301,913 (-)NCBIHuRef
CHM1_113113,800,717 - 113,831,888 (-)NCBICHM1_1
T2T-CHM13v2.013112,427,103 - 112,461,015 (-)NCBIT2T-CHM13v2.0
Pcid2
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39813,125,476 - 13,155,343 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl813,127,189 - 13,155,459 (-)EnsemblGRCm39 Ensembl
GRCm38813,075,476 - 13,105,343 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl813,077,189 - 13,105,459 (-)EnsemblGRCm38mm10GRCm38
MGSCv37813,077,525 - 13,105,343 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36813,077,167 - 13,105,382 (-)NCBIMGSCv36mm8
Celera813,244,463 - 13,272,258 (-)NCBICelera
Cytogenetic Map8A1.1NCBI
cM Map85.73NCBI
Pcid2
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_004955404618,092 - 639,704 (+)EnsemblChiLan1.0
ChiLan1.0NW_004955404618,092 - 639,424 (+)NCBIChiLan1.0ChiLan1.0
PCID2
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan113113,369,041 - 113,400,323 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01394,319,699 - 94,350,763 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.113113,388,251 - 113,419,523 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl13113,388,251 - 113,419,251 (-)Ensemblpanpan1.1panPan2
PCID2
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12260,602,440 - 60,623,811 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2260,602,888 - 60,623,719 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2260,314,829 - 60,336,177 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.02261,228,565 - 61,250,676 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl2261,228,122 - 61,309,216 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.12260,726,462 - 60,747,819 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.02260,728,651 - 60,750,011 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.02260,760,103 - 60,781,453 (-)NCBIUU_Cfam_GSD_1.0
Pcid2
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024404945195,488,082 - 195,511,764 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_004936472446,712 - 465,039 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_004936472440,440 - 464,116 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
PCID2
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1178,541,318 - 78,556,733 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11178,541,278 - 78,556,784 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21186,178,780 - 86,194,261 (+)NCBISscrofa10.2Sscrofa10.2susScr3
PCID2
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1391,163,158 - 91,212,450 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl391,177,463 - 91,211,735 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366604648,212,929 - 48,249,687 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Pcid2
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_004624793722,762 - 744,743 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_004624793722,743 - 744,824 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Pcid2
84 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:421
Count of miRNA genes:242
Interacting mature miRNAs:282
Transcripts:ENSRNOT00000044085
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
1600378Arunc4Aerobic running capacity QTL 40.03exercise endurance trait (VT:0002332)maximum distance run on treadmill (CMO:0001406)1638024580345693Rat
70205Gcr3Gastric cancer resistance QTL 32.3stomach morphology trait (VT:0000470)stomach tumor depth of invasion (CMO:0001888)161769679182635055Rat
70205Gcr3Gastric cancer resistance QTL 32.3stomach morphology trait (VT:0000470)stomach tumor depth of invasion (CMO:0001888)161769679182635055Rat
70205Gcr3Gastric cancer resistance QTL 32.3stomach morphology trait (VT:0000470)stomach tumor diameter (CMO:0001889)161769679182635055Rat
70205Gcr3Gastric cancer resistance QTL 32.3stomach morphology trait (VT:0000470)stomach tumor diameter (CMO:0001889)161769679182635055Rat
1578768Stresp22Stress response QTL 222.8thymus mass (VT:0004954)thymus wet weight (CMO:0000855)163528887080288870Rat
2293690Bss45Bone structure and strength QTL 455.130.0001lumbar vertebra morphology trait (VT:0010494)lumbar vertebra cortical cross-sectional area (CMO:0001690)163775215682752156Rat
2300163Bmd64Bone mineral density QTL 645.30.0001lumbar vertebra mineral mass (VT:0010511)volumetric bone mineral density (CMO:0001553)163775215682752156Rat
7205510Activ5Activity QTL 53.780.00028locomotor behavior trait (VT:0001392)number of entries into a discrete space in an experimental apparatus (CMO:0000960)164239634584729064Rat
8694429Bw164Body weight QTL 16450.001body lean mass (VT:0010483)lean tissue morphological measurement (CMO:0002184)165272646484729064Rat
8694364Abfw7Abdominal fat weight QTL 712.220.001visceral adipose mass (VT:0010063)abdominal fat pad weight to body weight ratio (CMO:0000095)165272646484729064Rat
7411648Foco22Food consumption QTL 22150.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)165272646484729064Rat
631525Pia14Pristane induced arthritis QTL 144.4joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)165571108783402471Rat

Markers in Region
RH130153  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21676,448,462 - 76,448,676 (+)MAPPERmRatBN7.2
Rnor_6.01681,782,798 - 81,783,011NCBIRnor6.0
Rnor_5.01681,268,165 - 81,268,378UniSTSRnor5.0
RGSC_v3.41681,305,643 - 81,305,856UniSTSRGSC3.4
Celera1674,254,495 - 74,254,708UniSTS
RH 3.4 Map16743.1UniSTS
Cytogenetic Map16q12.5UniSTS
RH133856  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21676,447,495 - 76,447,693 (+)MAPPERmRatBN7.2
Rnor_6.01681,781,831 - 81,782,028NCBIRnor6.0
Rnor_5.01681,267,198 - 81,267,395UniSTSRnor5.0
RGSC_v3.41681,304,676 - 81,304,873UniSTSRGSC3.4
Celera1674,253,528 - 74,253,725UniSTS
RH 3.4 Map16742.0UniSTS
Cytogenetic Map16q12.5UniSTS


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 3 24 34 18 19 18 1 1 74 32 36 11 1
Low 19 23 23 23 7 10 3 5 7
Below cutoff

Sequence


RefSeq Acc Id: ENSRNOT00000044085   ⟹   ENSRNOP00000049378
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1676,423,245 - 76,448,712 (+)Ensembl
Rnor_6.0 Ensembl1681,756,971 - 81,783,047 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000116016   ⟹   ENSRNOP00000082024
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1676,423,245 - 76,448,712 (+)Ensembl
RefSeq Acc Id: NM_001169144   ⟹   NP_001162615
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21676,423,245 - 76,448,712 (+)NCBI
Rnor_6.01681,757,582 - 81,783,047 (+)NCBI
Rnor_5.01681,242,949 - 81,268,414 (+)NCBI
RGSC_v3.41681,280,427 - 81,305,892 (+)RGD
Celera1674,229,279 - 74,254,744 (+)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_001162615 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAI60879 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000049378
  ENSRNOP00000049378.3
  ENSRNOP00000082024.1
RefSeq Acc Id: NP_001162615   ⟸   NM_001169144
- UniProtKB: B1H263 (UniProtKB/TrEMBL),   F1MAF5 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000049378   ⟸   ENSRNOT00000044085
RefSeq Acc Id: ENSRNOP00000082024   ⟸   ENSRNOT00000116016
Protein Domains
PCI

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-F1MAF5-F1-model_v2 AlphaFold F1MAF5 1-399 view protein structure

Transcriptome

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

Promoters
RGD ID:13700235
Promoter ID:EPDNEW_R10758
Type:multiple initiation site
Name:Pcid2_1
Description:PCI domain containing 2
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01681,757,573 - 81,757,633EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1307041 AgrOrtholog
BioCyc Gene G2FUF-10700 BioCyc
Ensembl Genes ENSRNOG00000025222 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000044085 ENTREZGENE
  ENSRNOT00000044085.5 UniProtKB/TrEMBL
  ENSRNOT00000116016.1 UniProtKB/TrEMBL
Gene3D-CATH 1.10.10.10 UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7380467 IMAGE-MGC_LOAD
InterPro Csn12-like UniProtKB/TrEMBL
  PCI_dom UniProtKB/TrEMBL
  WH-like_DNA-bd_sf UniProtKB/TrEMBL
KEGG Report rno:361182 UniProtKB/TrEMBL
MGC_CLONE MGC:188281 IMAGE-MGC_LOAD
NCBI Gene 361182 ENTREZGENE
PANTHER PCI DOMAIN-CONTAINING PROTEIN 2 UniProtKB/TrEMBL
  PTHR12732 UniProtKB/TrEMBL
Pfam PCI UniProtKB/TrEMBL
PhenoGen Pcid2 PhenoGen
PROSITE PCI UniProtKB/TrEMBL
RatGTEx ENSRNOG00000025222 RatGTEx
SMART PAM UniProtKB/TrEMBL
UniProt A0A8I5ZTF8_RAT UniProtKB/TrEMBL
  B1H263 ENTREZGENE, UniProtKB/TrEMBL
  F1MAF5 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2012-10-10 Pcid2  PCI domain containing 2  RGD1307041  similar to hypothetical protein FLJ11305  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-04-30 RGD1307041  similar to hypothetical protein FLJ11305   RGD1307041_predicted  similar to hypothetical protein FLJ11305 (predicted)  'predicted' is removed 2292626 APPROVED
2005-01-20 RGD1307041_predicted  similar to hypothetical protein FLJ11305 (predicted)  LOC361182_predicted    Symbol and Name status set to approved 1331353 APPROVED
2005-01-12 LOC361182_predicted  similar to hypothetical protein FLJ11305 (predicted)      Symbol and Name status set to provisional 70820 PROVISIONAL