Pabpc1l (poly(A) binding protein, cytoplasmic 1-like) - Rat Genome Database

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Gene: Pabpc1l (poly(A) binding protein, cytoplasmic 1-like) Rattus norvegicus
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Symbol: Pabpc1l
Name: poly(A) binding protein, cytoplasmic 1-like
RGD ID: 1563142
Description: Predicted to enable mRNA 3'-UTR binding activity; poly(A) binding activity; and poly(U) RNA binding activity. Predicted to be involved in positive regulation of translation. Predicted to act upstream of or within RNA metabolic process; nucleus localization; and oocyte maturation. Predicted to be located in cytoplasm. Predicted to be part of ribonucleoprotein complex. Predicted to be active in cytoplasmic stress granule; cytosol; and nucleus. Orthologous to human PABPC1L (poly(A) binding protein cytoplasmic 1 like); PARTICIPATES IN mRNA decay pathway; RNA degradation pathway; RNA transport pathway; INTERACTS WITH bisphenol A; methoxychlor; 2,3,7,8-tetrachlorodibenzodioxine (ortholog).
Type: protein-coding
RefSeq Status: MODEL
Previously known as: LOC296351; polyadenylate-binding protein 1-like; RGD1563142; similar to MGC89376 protein
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
GRCr83173,111,856 - 173,145,389 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl3173,112,904 - 173,146,038 (+)EnsemblGRCr8
mRatBN7.23152,692,825 - 152,725,997 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl3152,693,700 - 152,725,997 (+)EnsemblmRatBN7.2
Rnor_6.03160,410,733 - 160,447,073 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl3160,410,757 - 160,444,940 (+)Ensemblrn6Rnor6.0
Rnor_5.03166,597,627 - 166,629,983 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.43154,959,889 - 154,992,338 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera3151,342,191 - 151,376,854 (+)NCBICelera
Cytogenetic Map3q42NCBI
JBrowse:




Disease 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. GOA pipeline RGD automated data pipeline
4. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
5. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:22621333   PMID:23533145   PMID:26134869  


Genomics

Comparative Map Data
Pabpc1l
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr83173,111,856 - 173,145,389 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl3173,112,904 - 173,146,038 (+)EnsemblGRCr8
mRatBN7.23152,692,825 - 152,725,997 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl3152,693,700 - 152,725,997 (+)EnsemblmRatBN7.2
Rnor_6.03160,410,733 - 160,447,073 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl3160,410,757 - 160,444,940 (+)Ensemblrn6Rnor6.0
Rnor_5.03166,597,627 - 166,629,983 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.43154,959,889 - 154,992,338 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera3151,342,191 - 151,376,854 (+)NCBICelera
Cytogenetic Map3q42NCBI
PABPC1L
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh382044,910,060 - 44,939,316 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl2044,910,060 - 44,959,035 (+)Ensemblhg38GRCh38
GRCh372043,538,701 - 43,567,957 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 362042,972,117 - 43,001,376 (+)NCBIBuild 36Build 36hg18NCBI36
Build 342042,994,233 - 43,021,087NCBI
Celera2040,247,341 - 40,276,594 (+)NCBICelera
Cytogenetic Map20q13.12NCBI
HuRef2040,280,535 - 40,309,641 (+)NCBIHuRef
CHM1_12043,441,629 - 43,470,743 (+)NCBICHM1_1
T2T-CHM13v2.02046,645,923 - 46,675,185 (+)NCBIT2T-CHM13v2.0
Pabpc1l
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm392163,866,685 - 163,892,458 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl2163,867,370 - 163,892,458 (+)EnsemblGRCm39 EnsemblGRCm39
GRCm382164,024,770 - 164,050,538 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl2164,025,450 - 164,050,538 (+)Ensemblmm10GRCm38
MGSCv372163,851,186 - 163,876,274 (+)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv362163,716,922 - 163,741,480 (+)NCBIMGSCv36mm8
Celera2169,955,661 - 169,980,596 (+)NCBICelera
Cytogenetic Map2H3NCBI
cM Map284.6NCBI
Pabpc1l
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495544512,422,204 - 12,450,024 (-)Ensembl
ChiLan1.0NW_00495544512,425,738 - 12,450,830 (-)NCBIChiLan1.0ChiLan1.0
PABPC1L
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v22150,642,848 - 50,672,499 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan12050,635,980 - 50,665,604 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v02041,240,430 - 41,270,036 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.12042,333,592 - 42,362,510 (+)NCBIPanPan1.1PanPan1.1panPan2
PanPan1.1 Ensembl2042,333,593 - 42,375,850 (+)EnsemblpanPan2panpan1.1
PABPC1L
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12432,327,479 - 32,348,964 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2432,327,494 - 32,349,071 (+)EnsemblcanFam3CanFam3.1
Dog10K_Boxer_Tasha2431,973,114 - 31,994,462 (+)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.02433,038,733 - 33,059,922 (+)NCBIROS_Cfam_1.0ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl2433,016,085 - 33,059,979 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.12432,299,944 - 32,321,262 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.02432,414,644 - 32,436,215 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.02432,956,572 - 32,977,933 (+)NCBIUU_Cfam_GSD_1.0UU_Cfam_GSD_1.0
Pabpc1l
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024408640192,352,267 - 192,378,046 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049365147,809,080 - 7,830,246 (-)EnsemblSpeTri2.0 Ensembl
SpeTri2.0NW_0049365147,809,030 - 7,831,606 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
PABPC1L
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1747,321,264 - 47,350,556 (+)EnsemblsusScr11Sscrofa11.1
Sscrofa11.11747,321,259 - 47,351,905 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21752,817,476 - 52,847,301 (+)NCBISscrofa10.2Sscrofa10.2susScr3
PABPC1L
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1218,872,217 - 18,904,492 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl218,872,021 - 18,902,991 (-)EnsemblChlSab1.1 EnsemblchlSab2Vervet-AGM
Vero_WHO_p1.0NW_02366605067,521,312 - 67,571,391 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Pabpc1l
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046247909,545,145 - 9,570,872 (-)EnsemblHetGla_female_1.0 EnsemblhetGla2HetGla_female_1.0 Ensembl
HetGla 1.0NW_0046247909,545,719 - 9,572,447 (-)NCBIHetGla 1.0HetGla 1.0hetGla2
Pabpc1l
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v15153,926,556 - 153,953,078 (-)NCBIRrattus_CSIRO_v1

miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:42
Count of miRNA genes:39
Interacting mature miRNAs:42
Transcripts:ENSRNOT00000055172
Prediction methods: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 (GRCr8)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
12879876Bw182Body weight QTL 1820.003body mass (VT:0001259)body weight (CMO:0000012)3141555229186555229Rat
2301411Bp320Blood pressure QTL 3200.001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)3141555229186555229Rat
1582233Insul10Insulin level QTL 105.40.0015blood insulin amount (VT:0001560)serum insulin level times blood glucose level (CMO:0002040)3133259579178259579Rat
1300113Bp176Blood pressure QTL 1763.9arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)3166376089177728348Rat
12879872Cm97Cardiac mass QTL 970.001heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)3141555229186555229Rat
12879873Cm96Cardiac mass QTL 960.001heart mass (VT:0007028)heart wet weight to body weight ratio (CMO:0002408)3141555229186555229Rat
1578653Vnigr3Vascular neointimal growth QTL 33.1artery morphology trait (VT:0002191)artery neointimal hyperplastic lesion area (CMO:0001414)3151075912189428310Rat
2302373Gluco39Glucose level QTL 395.01blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)3129154923182114333Rat
12879874Cm98Cardiac mass QTL 980.005heart right ventricle mass (VT:0007033)heart right ventricle weight to body weight ratio (CMO:0000914)3141555229186555229Rat
12879875Kidm64Kidney mass QTL 640.001kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)3141555229186555229Rat
1298068Bp167Blood pressure QTL 1670.004arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)3161492708189428310Rat
70216Cm14Cardiac mass QTL 142.1heart mass (VT:0007028)heart wet weight (CMO:0000069)351581665184004958Rat
8552791Vie2Viral induced encephalitis QTL 24.1brain integrity trait (VT:0010579)encephalitis incidence/prevalence measurement (CMO:0002361)3166376089189428310Rat
61335Bp20Blood pressure QTL 203arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)3161799493176036425Rat
1578754Stresp16Stress response QTL 1640.001blood renin amount (VT:0003349)plasma renin activity level (CMO:0000116)3133134628178134628Rat
1331726Bp208Blood pressure QTL 2083.129arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)3161799270187311134Rat
1582213Insul6Insulin level QTL 63.70.0009blood insulin amount (VT:0001560)calculated serum insulin level (CMO:0000359)3155759447189428310Rat
1598854Memor10Memory QTL 102exploratory behavior trait (VT:0010471)average horizontal distance between subject and target during voluntary locomotion in an experimental apparatus (CMO:0002674)3166376089189428310Rat
9589106Insul23Insulin level QTL 2313.860.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)3152055202189428310Rat
10755461Coatc16Coat color QTL 16coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)3142898802187898802Rat
8662816Vetf4Vascular elastic tissue fragility QTL 44renal artery integrity trait (VT:0010642)number of ruptures of the internal elastic lamina of the renal arteries (CMO:0002563)379649560177741895Rat
1559282Emca5Estrogen-induced mammary cancer QTL 53.9mammary gland integrity trait (VT:0010552)percentage of study population developing mammary tumors during a period of time (CMO:0000948)3145335553189428310Rat
1582256Insul9Insulin level QTL 94.40.0016blood insulin amount (VT:0001560)absolute change in serum insulin level (CMO:0002038)3155759447189428310Rat
1576306Schws3Schwannoma susceptibility QTL 30.001nervous system integrity trait (VT:0010566)percentage of study population developing trigeminal nerve neurilemmomas during a period of time (CMO:0002017)3139299381184299381Rat
1300159Kidm4Kidney mass QTL 43.83kidney mass (VT:0002707)right kidney wet weight to body weight ratio (CMO:0001953)3141508991177728348Rat
2301971Cm71Cardiac mass QTL 714.63heart left ventricle mass (VT:0007031)heart left ventricle weight (CMO:0000776)3131036586176036586Rat
631673Iddm13Insulin dependent diabetes mellitus QTL 131.30.663blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)3137114333182114333Rat
1582248Insul7Insulin level QTL 73.90.0041blood insulin amount (VT:0001560)calculated serum insulin level (CMO:0000359)3155759447189428310Rat
2301970Bw81Body weight QTL 815.19body mass (VT:0001259)body weight (CMO:0000012)3131036586176036586Rat
1578666Vnigr1Vascular neointimal growth QTL 14.6artery morphology trait (VT:0002191)artery lumen area (CMO:0001409)3151075912189428310Rat
1578656Vnigr2Vascular neointimal growth QTL 24.2artery morphology trait (VT:0002191)lesioned artery residual lumen area (CMO:0001417)3151075912189428310Rat
12879871Am7Aortic mass QTL 70.001aorta mass (VT:0002845)aorta weight to aorta length to body weight ratio (CMO:0002722)3141555229186555229Rat
631541Bp81Blood pressure QTL 814arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)3144575244189428310Rat

Markers in Region
RH127744  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.23152,729,364 - 152,729,549 (+)MAPPERmRatBN7.2
Rnor_6.03160,448,317 - 160,448,501NCBIRnor6.0
Rnor_6.03160,438,256 - 160,438,440NCBIRnor6.0
Rnor_5.03166,632,910 - 166,633,094UniSTSRnor5.0
Rnor_5.03166,623,859 - 166,624,043UniSTSRnor5.0
RGSC_v3.43154,995,706 - 154,995,890UniSTSRGSC3.4
Celera3151,378,101 - 151,378,285UniSTS
RH 3.4 Map31421.2UniSTS
Cytogenetic Map3q42UniSTS


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
7 5 11 34 25 30 5 39 5 3 89 60 1 28 13 42 25 2 2

Sequence


Ensembl Acc Id: ENSRNOT00000055172   ⟹   ENSRNOP00000052046
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl3173,112,904 - 173,145,389 (+)Ensembl
mRatBN7.2 Ensembl3152,693,700 - 152,725,997 (+)Ensembl
Rnor_6.0 Ensembl3160,410,757 - 160,444,940 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000140965   ⟹   ENSRNOP00000108058
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl3173,112,904 - 173,146,038 (+)Ensembl
RefSeq Acc Id: XM_063285213   ⟹   XP_063141283
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr83173,111,856 - 173,145,389 (+)NCBI
Protein Sequences
Protein RefSeqs XP_063141283 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDL96553 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000052046
  ENSRNOP00000052046.4
  ENSRNOP00000108058.1
Ensembl Acc Id: ENSRNOP00000052046   ⟸   ENSRNOT00000055172
RefSeq Acc Id: XP_063141283   ⟸   XM_063285213
- UniProtKB: D3ZAS7 (UniProtKB/TrEMBL)
Ensembl Acc Id: ENSRNOP00000108058   ⟸   ENSRNOT00000140965
Protein Domains
PABC   RRM

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D3ZAS7-F1-model_v2 AlphaFold D3ZAS7 1-607 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:1563142 AgrOrtholog
BioCyc Gene G2FUF-46885 BioCyc
Ensembl Genes ENSRNOG00000012750 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000055172 ENTREZGENE
  ENSRNOT00000055172.5 UniProtKB/TrEMBL
  ENSRNOT00000140965.1 UniProtKB/TrEMBL
Gene3D-CATH 3.30.70.330 UniProtKB/TrEMBL
  c-terminal domain of poly(a) binding protein UniProtKB/TrEMBL
InterPro Euk_RNA-bind_prot UniProtKB/TrEMBL
  Nucleotide-bd_a/b_plait_sf UniProtKB/TrEMBL
  PABP-dom UniProtKB/TrEMBL
  PABP_1234 UniProtKB/TrEMBL
  PABP_HYD UniProtKB/TrEMBL
  PABP_RRM1 UniProtKB/TrEMBL
  RBD_domain_sf UniProtKB/TrEMBL
  RRM2_I_PABPs UniProtKB/TrEMBL
  RRM_dom_euk UniProtKB/TrEMBL
  RRM_RNP1 UniProtKB/TrEMBL
NCBI Gene 296351 ENTREZGENE
PANTHER OS02G0815200 PROTEIN UniProtKB/TrEMBL
  RRM DOMAIN-CONTAINING PROTEIN UniProtKB/TrEMBL
Pfam PABP UniProtKB/TrEMBL
  RRM_1 UniProtKB/TrEMBL
PhenoGen Pabpc1l PhenoGen
PROSITE PABC UniProtKB/TrEMBL
  RRM UniProtKB/TrEMBL
RatGTEx ENSRNOG00000012750 RatGTEx
SMART PolyA UniProtKB/TrEMBL
  RRM UniProtKB/TrEMBL
  RRM_1 UniProtKB/TrEMBL
Superfamily-SCOP PABP_HYD UniProtKB/TrEMBL
  SSF54928 UniProtKB/TrEMBL
UniProt A0ABK0LBR6_RAT UniProtKB/TrEMBL
  D3ZAS7 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2010-05-05 Pabpc1l  poly(A) binding protein, cytoplasmic 1-like  RGD1563142  similar to MGC89376 protein  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-04-30 RGD1563142  similar to MGC89376 protein   RGD1563142_predicted  similar to MGC89376 protein (predicted)  'predicted' is removed 2292626 APPROVED
2006-03-07 RGD1563142_predicted  similar to MGC89376 protein (predicted)  LOC296351  similar to MGC89376 protein  Symbol and Name status set to approved 1299863 APPROVED
2006-02-09 LOC296351  similar to MGC89376 protein      Symbol and Name status set to provisional 70820 PROVISIONAL