Pabpc5 (poly A binding protein, cytoplasmic 5) - Rat Genome Database

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Gene: Pabpc5 (poly A binding protein, cytoplasmic 5) Rattus norvegicus
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Symbol: Pabpc5
Name: poly A binding protein, cytoplasmic 5
RGD ID: 1587661
Description: Predicted to enable mRNA 3'-UTR binding activity; poly(A) binding activity; and poly(U) RNA binding activity. Predicted to be located in mitochondrial matrix. Predicted to be part of ribonucleoprotein complex. Predicted to be active in cytoplasmic stress granule; cytosol; and nucleus. Orthologous to human PABPC5 (poly(A) binding protein cytoplasmic 5); PARTICIPATES IN mRNA decay pathway; RNA degradation pathway; RNA transport pathway; INTERACTS WITH bisphenol A; trichloroethene; benzo[a]pyrene (ortholog).
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: LOC688518; poly A binding protein, cytoplasmic 5-like; polyadenylate-binding protein 5; similar to poly A binding protein, cytoplasmic 5
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Black Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8X89,858,502 - 89,862,454 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 EnsemblX89,858,427 - 89,860,487 (+)EnsemblGRCr8
mRatBN7.2X85,637,763 - 85,641,235 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 EnsemblX85,638,574 - 85,639,722 (+)EnsemblmRatBN7.2
UTH_Rnor_SHR_UtxX87,294,548 - 87,295,696 (+)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0X90,728,025 - 90,729,173 (+)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0X88,285,824 - 88,286,972 (+)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0X92,130,292 - 92,133,756 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 EnsemblX92,131,209 - 92,132,357 (+)Ensemblrn6Rnor6.0
Rnor_5.0X92,037,490 - 92,038,638 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.4X109,402,246 - 109,404,584 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
CeleraX86,791,881 - 86,793,029 (+)NCBICelera
Cytogenetic MapXq31NCBI
JBrowse:




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

Cellular Component

Molecular Function

Molecular Pathway 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. KEGG Annotation Import Pipeline Pipeline to import KEGG annotations from KEGG into RGD
3. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions

Genomics

Comparative Map Data
Pabpc5
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8X89,858,502 - 89,862,454 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 EnsemblX89,858,427 - 89,860,487 (+)EnsemblGRCr8
mRatBN7.2X85,637,763 - 85,641,235 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 EnsemblX85,638,574 - 85,639,722 (+)EnsemblmRatBN7.2
UTH_Rnor_SHR_UtxX87,294,548 - 87,295,696 (+)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0X90,728,025 - 90,729,173 (+)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0X88,285,824 - 88,286,972 (+)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0X92,130,292 - 92,133,756 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 EnsemblX92,131,209 - 92,132,357 (+)Ensemblrn6Rnor6.0
Rnor_5.0X92,037,490 - 92,038,638 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.4X109,402,246 - 109,404,584 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
CeleraX86,791,881 - 86,793,029 (+)NCBICelera
Cytogenetic MapXq31NCBI
PABPC5
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38X91,434,839 - 91,438,584 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 EnsemblX91,434,595 - 91,438,584 (+)Ensemblhg38GRCh38
GRCh37X90,689,838 - 90,693,583 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36X90,576,253 - 90,580,239 (+)NCBIBuild 36Build 36hg18NCBI36
Build 34X90,495,741 - 90,499,727NCBI
CeleraX91,182,192 - 91,186,295 (+)NCBICelera
Cytogenetic MapXq21.31NCBI
HuRefY2,355,075 - 2,359,061 (+)NCBIHuRef
CHM1_1X90,582,274 - 90,586,260 (+)NCBICHM1_1
T2T-CHM13v2.0X89,886,956 - 89,890,701 (+)NCBIT2T-CHM13v2.0
Pabpc5
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39X118,836,893 - 118,839,862 (+)NCBIGRCm39GRCm39mm39
GRCm39 EnsemblX118,836,893 - 118,839,862 (+)EnsemblGRCm39 EnsemblGRCm39
GRCm38X119,927,196 - 119,930,165 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 EnsemblX119,927,196 - 119,930,165 (+)Ensemblmm10GRCm38
MGSCv37X117,040,805 - 117,043,774 (+)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv36X116,044,140 - 116,047,109 (+)NCBIMGSCv36mm8
CeleraX106,515,330 - 106,518,299 (+)NCBICelera
Cytogenetic MapXE1NCBI
cM MapX49.58NCBI
Pabpc5
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049555252,847,458 - 2,849,836 (-)Ensembl
ChiLan1.0NW_0049555252,847,458 - 2,849,836 (-)NCBIChiLan1.0ChiLan1.0
PABPC5
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2X91,012,326 - 91,015,349 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1X91,015,931 - 91,023,650 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0X80,625,721 - 80,633,345 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1X90,797,014 - 90,801,001 (+)NCBIPanPan1.1PanPan1.1panPan2
PanPan1.1 EnsemblX90,797,994 - 90,799,142 (+)EnsemblpanPan2panpan1.1
PABPC5
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1X68,490,296 - 68,508,088 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Dog10K_Boxer_TashaX59,266,158 - 59,286,391 (+)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.0X69,831,333 - 69,851,587 (+)NCBIROS_Cfam_1.0ROS_Cfam_1.0
ROS_Cfam_1.0 EnsemblX69,831,472 - 69,835,153 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1X67,472,369 - 67,492,938 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0X69,114,270 - 69,134,528 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0X68,708,118 - 68,728,370 (+)NCBIUU_Cfam_GSD_1.0UU_Cfam_GSD_1.0
Pabpc5
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2X71,870,352 - 71,877,674 (+)NCBIHiC_Itri_2
SpeTri2.0NW_0049366492,195,918 - 2,201,480 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
LOC100518351
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 EnsemblX74,142,566 - 74,145,719 (+)EnsemblsusScr11Sscrofa11.1
Sscrofa11.1X74,141,707 - 74,145,941 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2X95,053,194 - 95,056,290 (-)NCBISscrofa10.2Sscrofa10.2susScr3
PABPC5
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1X80,112,990 - 80,117,003 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 EnsemblX80,113,979 - 80,115,124 (+)EnsemblChlSab1.1 EnsemblchlSab2Vervet-AGM
Vero_WHO_p1.0NW_023666067593,301 - 600,503 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Pabpc5
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046249112,722,619 - 2,725,593 (+)NCBIHetGla 1.0HetGla 1.0hetGla2
Pabpc5
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v1X49,469,182 - 49,471,170 (-)NCBIRrattus_CSIRO_v1

Variants

.
Variants in Pabpc5
9 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:93
Count of miRNA genes:82
Interacting mature miRNAs:88
Transcripts:ENSRNOT00000004462
Prediction methods:Microtar, 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 (GRCr8)
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)X80434318125434318Rat
738035Stresp1Stress response QTL 14.960.000011stress-related behavior trait (VT:0010451)defensive burying - copingX45182909117740458Rat
1598837Memor13Memory QTL 133.2exploratory behavior trait (VT:0010471)difference between duration of physical contact or close proximity of test subject and social stimulus during sample phase and test phase (CMO:0002678)X4493088389930883Rat

Markers in Region
UniSTS:479188  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2X85,638,715 - 85,639,328 (+)MAPPERmRatBN7.2
Rnor_6.0X92,131,351 - 92,131,963NCBIRnor6.0
Rnor_5.0X92,037,632 - 92,038,244UniSTSRnor5.0
RGSC_v3.4X109,402,539 - 109,403,151UniSTSRGSC3.4
CeleraX86,792,023 - 86,792,635UniSTS


Expression

RNA-SEQ Expression

alimentary part of gastrointestinal system
appendage
circulatory system
ectoderm
endocrine system
endoderm
exocrine system
hemolymphoid system
hepatobiliary system
integumental system
mesenchyme
mesoderm
musculoskeletal system
nervous system
renal system
reproductive system
respiratory system
sensory system
visual system
3 8 37 120 22 17 5 12 5 3 101 66 5 105 19 67 12 8 8

Sequence


Ensembl Acc Id: ENSRNOT00000004462   ⟹   ENSRNOP00000004462
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 EnsemblX89,858,427 - 89,860,487 (+)Ensembl
mRatBN7.2 EnsemblX85,638,574 - 85,639,722 (+)Ensembl
Rnor_6.0 EnsemblX92,131,209 - 92,132,357 (+)Ensembl
RefSeq Acc Id: NM_001110366   ⟹   NP_001103836
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8X89,859,350 - 89,860,498 (+)NCBI
mRatBN7.2X85,638,574 - 85,639,722 (+)NCBI
Rnor_6.0X92,131,209 - 92,132,357 (+)NCBI
Rnor_5.0X92,037,490 - 92,038,638 (+)NCBI
RGSC_v3.4X109,402,246 - 109,404,584 (+)RGD
CeleraX86,791,881 - 86,793,029 (+)NCBI
Sequence:
RefSeq Acc Id: XM_008773376   ⟹   XP_008771598
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8X89,858,502 - 89,862,454 (+)NCBI
mRatBN7.2X85,637,763 - 85,641,235 (+)NCBI
Rnor_6.0X92,130,292 - 92,133,756 (+)NCBI
Sequence:
Protein Sequences
Protein RefSeqs NP_001103836 (Get FASTA)   NCBI Sequence Viewer  
  XP_008771598 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDM07061 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000004462
  ENSRNOP00000004462.6
RefSeq Acc Id: NP_001103836   ⟸   NM_001110366
- UniProtKB: D4A5H0 (UniProtKB/TrEMBL),   A6IVB9 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_008771598   ⟸   XM_008773376
- Peptide Label: isoform X1
- Sequence:
Ensembl Acc Id: ENSRNOP00000004462   ⟸   ENSRNOT00000004462
Protein Domains
RRM

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D4A5H0-F1-model_v2 AlphaFold D4A5H0 1-382 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:1587661 AgrOrtholog
BioCyc Gene G2FUF-1775 BioCyc
Ensembl Genes ENSRNOG00000003354 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000004462 ENTREZGENE
  ENSRNOT00000004462.8 UniProtKB/TrEMBL
Gene3D-CATH 3.30.70.330 UniProtKB/TrEMBL
InterPro Nucleotide-bd_a/b_plait_sf UniProtKB/TrEMBL
  PABP_RRM1 UniProtKB/TrEMBL
  RBD_domain_sf UniProtKB/TrEMBL
  RRM2_I_PABPs UniProtKB/TrEMBL
  RRM_dom UniProtKB/TrEMBL
  RRM_dom_euk UniProtKB/TrEMBL
KEGG Report rno:688518 UniProtKB/TrEMBL
NCBI Gene 688518 ENTREZGENE
PANTHER RNA BINDING PROTEIN UniProtKB/TrEMBL
Pfam RRM_1 UniProtKB/TrEMBL
PhenoGen Pabpc5 PhenoGen
PROSITE RRM UniProtKB/TrEMBL
RatGTEx ENSRNOG00000003354 RatGTEx
SMART RRM UniProtKB/TrEMBL
  RRM_1 UniProtKB/TrEMBL
Superfamily-SCOP SSF54928 UniProtKB/TrEMBL
UniProt A6IVB9 ENTREZGENE, UniProtKB/TrEMBL
  D4A5H0 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2013-05-24 Pabpc5  poly A binding protein, cytoplasmic 5  LOC100360473  poly A binding protein, cytoplasmic 5-like  Data merged from RGD:2322083 1643240 APPROVED
2010-05-06 LOC100360473  poly A binding protein, cytoplasmic 5-like      Symbol and Name status set to provisional 70820 PROVISIONAL
2008-03-05 Pabpc5  poly A binding protein, cytoplasmic 5  LOC688518  similar to poly A binding protein, cytoplasmic 5  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-01-09 LOC688518  similar to poly A binding protein, cytoplasmic 5  LOC302768  similar to poly A binding protein, cytoplasmic 5  Data merged from RGD:1584984 1643240 APPROVED
2006-11-19 LOC688518  similar to poly A binding protein, cytoplasmic 5      Symbol and Name status set to provisional 70820 PROVISIONAL
2006-11-19 LOC302768  similar to poly A binding protein, cytoplasmic 5      Symbol and Name status set to provisional 70820 PROVISIONAL