Pin4 (peptidylprolyl cis/trans isomerase, NIMA-interacting 4) - Rat Genome Database

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Gene: Pin4 (peptidylprolyl cis/trans isomerase, NIMA-interacting 4) Rattus norvegicus
Analyze
Symbol: Pin4
Name: peptidylprolyl cis/trans isomerase, NIMA-interacting 4 (Ensembl:peptidyl-prolyl cis/trans isomerase, NIMA-interacting, 4 (parvulin))
RGD ID: 1590326
Description: Predicted to enable bent DNA binding activity and double-stranded DNA binding activity. Predicted to be involved in localization and rRNA processing. Predicted to be located in several cellular components, including mitochondrial matrix; nuclear lumen; and spindle. Predicted to be part of preribosome. Predicted to be active in nucleus. Orthologous to human PIN4 (peptidylprolyl cis/trans isomerase, NIMA-interacting 4); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; Cuprizon; tetrachloromethane.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: LOC684441; peptidyl-prolyl cis-trans isomerase NIMA-interacting 4; protein (peptidylprolyl cis/trans isomerase) NIMA-interacting, 4 (parvulin); similar to Peptidyl-prolyl cis-trans isomerase NIMA-interacting 4 (Rotamase Pin4) (PPIase Pin4)
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
mRatBN7.2X67,232,006 - 67,238,707 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 EnsemblX67,232,081 - 67,238,702 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1852,213,206 - 52,213,661 (-)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.0X72,215,663 - 72,222,306 (+)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.01850,719,086 - 50,719,541 (-)NCBIRnor_WKY
Rnor_6.0X72,004,413 - 72,011,667 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 EnsemblX72,004,482 - 72,011,664 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0X72,849,341 - 72,856,082 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4X90,182,412 - 90,188,371 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
CeleraX67,585,854 - 67,592,558 (+)NCBICelera
Cytogenetic MapXq22NCBI
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

Biological Process
localization  (ISO)
rRNA processing  (IBA,ISO)

Cellular Component
chromosome  (ISO)
cytoplasm  (ISO)
mitochondrial matrix  (ISO)
nucleolus  (ISO)
nucleoplasm  (ISO)
nucleus  (IBA,ISO)
preribosome  (ISO)
spindle  (ISO)

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. GOA pipeline RGD automated data pipeline
3. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:12144781   PMID:17875217   PMID:19369196   PMID:22681889   PMID:23376485  


Genomics

Comparative Map Data
Pin4
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2X67,232,006 - 67,238,707 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 EnsemblX67,232,081 - 67,238,702 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1852,213,206 - 52,213,661 (-)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.0X72,215,663 - 72,222,306 (+)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.01850,719,086 - 50,719,541 (-)NCBIRnor_WKY
Rnor_6.0X72,004,413 - 72,011,667 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 EnsemblX72,004,482 - 72,011,664 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0X72,849,341 - 72,856,082 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4X90,182,412 - 90,188,371 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
CeleraX67,585,854 - 67,592,558 (+)NCBICelera
Cytogenetic MapXq22NCBI
PIN4
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38X72,181,676 - 72,263,964 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 EnsemblX72,181,353 - 72,302,926 (+)EnsemblGRCh38hg38GRCh38
GRCh37X71,401,526 - 71,483,814 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36X71,318,251 - 71,334,666 (+)NCBINCBI36Build 36hg18NCBI36
Build 34X71,184,546 - 71,200,961NCBI
CeleraX71,749,520 - 71,827,026 (+)NCBICelera
Cytogenetic MapXq13.1NCBI
HuRefX65,156,426 - 65,238,895 (+)NCBIHuRef
CHM1_1X71,294,590 - 71,376,836 (+)NCBICHM1_1
T2T-CHM13v2.0X70,614,580 - 70,696,859 (+)NCBIT2T-CHM13v2.0
Pin4
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39X101,163,075 - 101,171,276 (+)NCBIGRCm39GRCm39mm39
GRCm39 EnsemblX101,163,053 - 101,171,275 (+)EnsemblGRCm39 Ensembl
GRCm38X102,119,469 - 102,127,673 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 EnsemblX102,119,447 - 102,127,669 (+)EnsemblGRCm38mm10GRCm38
MGSCv37X99,314,804 - 99,323,012 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36X98,322,182 - 98,334,891 (+)NCBIMGSCv36mm8
CeleraX89,031,383 - 89,039,555 (+)NCBICelera
Cytogenetic MapXDNCBI
Pin4
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495547511,562,982 - 11,581,042 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495547511,563,379 - 11,577,133 (+)NCBIChiLan1.0ChiLan1.0
PIN4
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1X71,858,641 - 71,874,633 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0X61,418,250 - 61,502,191 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1X71,503,148 - 71,586,017 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 EnsemblX71,503,148 - 71,586,017 (+)Ensemblpanpan1.1panPan2
LOC100687619
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12817,935,504 - 17,935,947 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2818,105,658 - 18,106,071 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.02818,424,158 - 18,424,571 (+)NCBIROS_Cfam_1.0
UMICH_Zoey_3.12817,959,442 - 17,959,855 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.02817,996,740 - 17,997,153 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.02818,128,344 - 18,128,757 (+)NCBIUU_Cfam_GSD_1.0
Pin4
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2X45,689,380 - 45,701,487 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_00493695936,136 - 48,508 (-)EnsemblSpeTri2.0
SpeTri2.0NW_00493695936,374 - 48,480 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
PIN4
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 EnsemblX58,069,793 - 58,082,239 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1X58,069,758 - 58,082,243 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2X65,779,503 - 65,791,485 (+)NCBISscrofa10.2Sscrofa10.2susScr3
PIN4
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1X61,994,237 - 62,008,537 (+)NCBIChlSab1.1ChlSab1.1chlSab2
Vero_WHO_p1.0NW_0236660653,849,593 - 3,865,051 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Pin4
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046249032,424,620 - 2,443,648 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046249032,424,424 - 2,439,815 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Pin4
3 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:31
Count of miRNA genes:31
Interacting mature miRNAs:31
Transcripts:ENSRNOT00000073157
Prediction methods:Miranda, Pita, 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 (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
61430Cia18Collagen induced arthritis QTL 183.1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)X14843113120568734Rat
1598837Memor13Memory QTL 133.2exploratory behavior trait (VT:0010471)difference between time of physical contact/close proximity of test subject and social stimulus during sample phase and test phase (CMO:0002678)X41052407146860749Rat
738035Stresp1Stress response QTL 14.960.000011stress-related behavior trait (VT:0010451)defensive burying - copingX41304447112935181Rat
61431Cia19Collagen induced arthritis QTL 194.4joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)X65612192120568734Rat

Markers in Region
RH80498  
Rat AssemblyChrPosition (strand)SourceJBrowse
CeleraX67,592,383 - 67,592,505UniSTS
Celera2013,001,028 - 13,001,145UniSTS
Cytogenetic Map20p12UniSTS


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 40 57 41 19 41 8 11 74 35 41 11 8
Low 3
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000073157   ⟹   ENSRNOP00000067375
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 EnsemblX67,232,081 - 67,238,702 (+)Ensembl
Rnor_6.0 EnsemblX72,004,482 - 72,011,664 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000096972   ⟹   ENSRNOP00000093975
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 EnsemblX67,233,967 - 67,238,702 (+)Ensembl
RefSeq Acc Id: XM_003752069   ⟹   XP_003752117
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X67,232,006 - 67,238,707 (+)NCBI
Rnor_6.0X72,004,423 - 72,011,667 (+)NCBI
Rnor_5.0X72,849,341 - 72,856,082 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006257122   ⟹   XP_006257184
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X67,232,024 - 67,238,707 (+)NCBI
Rnor_6.0X72,004,413 - 72,011,667 (+)NCBI
Rnor_5.0X72,849,341 - 72,856,082 (+)NCBI
Sequence:
RefSeq Acc Id: XM_039100217   ⟹   XP_038956145
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X67,232,341 - 67,238,707 (+)NCBI
RefSeq Acc Id: XM_039100218   ⟹   XP_038956146
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X67,232,897 - 67,238,707 (+)NCBI
RefSeq Acc Id: XM_039100219   ⟹   XP_038956147
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X67,232,842 - 67,238,707 (+)NCBI
Reference Sequences
RefSeq Acc Id: XP_003752117   ⟸   XM_003752069
- Peptide Label: isoform X2
- UniProtKB: M0RCP9 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006257184   ⟸   XM_006257122
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: ENSRNOP00000067375   ⟸   ENSRNOT00000073157
RefSeq Acc Id: XP_038956145   ⟸   XM_039100217
- Peptide Label: isoform X3
RefSeq Acc Id: XP_038956147   ⟸   XM_039100219
- Peptide Label: isoform X3
RefSeq Acc Id: XP_038956146   ⟸   XM_039100218
- Peptide Label: isoform X3
RefSeq Acc Id: ENSRNOP00000093975   ⟸   ENSRNOT00000096972
Protein Domains
PpiC

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-M0RCP9-F1-model_v2 AlphaFold M0RCP9 1-131 view protein structure

Transcriptome

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

Promoters
RGD ID:13701883
Promoter ID:EPDNEW_R12405
Type:initiation region
Name:Pin4_1
Description:peptidylprolyl cis/trans isomerase, NIMA-interacting 4
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_6.0X72,004,525 - 72,004,585EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1590326 AgrOrtholog
BioCyc Gene G2FUF-2082 BioCyc
Ensembl Genes ENSRNOG00000050051 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000067375 ENTREZGENE
  ENSRNOP00000067375.2 UniProtKB/TrEMBL
  ENSRNOP00000093975 ENTREZGENE
  ENSRNOP00000093975.1 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000073157 ENTREZGENE
  ENSRNOT00000073157.2 UniProtKB/TrEMBL
  ENSRNOT00000096972 ENTREZGENE
  ENSRNOT00000096972.1 UniProtKB/TrEMBL
Gene3D-CATH 3.10.50.40 UniProtKB/TrEMBL
InterPro PIN4 UniProtKB/TrEMBL
  PPIase_dom_sf UniProtKB/TrEMBL
  PPIase_PpiC UniProtKB/TrEMBL
KEGG Report rno:684441 UniProtKB/TrEMBL
NCBI Gene 684441 ENTREZGENE
PANTHER PEPTIDYL-PROLYL CIS-TRANS ISOMERASE NIMA-INTERACTING 4 UniProtKB/TrEMBL
  PTHR45995 UniProtKB/TrEMBL
Pfam Rotamase_3 UniProtKB/TrEMBL
PhenoGen Pin4 PhenoGen
PROSITE PPIC_PPIASE_2 UniProtKB/TrEMBL
Superfamily-SCOP FKBP-like UniProtKB/TrEMBL
UniProt A0A8I6GKI8_RAT UniProtKB/TrEMBL
  M0RCP9 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2015-03-16 Pin4  peptidylprolyl cis/trans isomerase, NIMA-interacting 4  Pin4  protein (peptidylprolyl cis/trans isomerase) NIMA-interacting, 4 (parvulin)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2013-08-13 Pin4  protein (peptidylprolyl cis/trans isomerase) NIMA-interacting, 4 (parvulin)  LOC684441  similar to Peptidyl-prolyl cis-trans isomerase NIMA-interacting 4 (Rotamase Pin4) (PPIase Pin4)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2013-08-13 Pin4  protein (peptidylprolyl cis/trans isomerase) NIMA-interacting, 4 (parvulin)  Pin4  protein (peptidylprolyl cis/trans isomerase) NIMA-interacting, 4 (parvulin)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-11-20 LOC684441  similar to Peptidyl-prolyl cis-trans isomerase NIMA-interacting 4 (Rotamase Pin4) (PPIase Pin4)      Symbol and Name status set to provisional 70820 PROVISIONAL