Pabpn1l (PABPN1 like) - Rat Genome Database

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Gene: Pabpn1l (PABPN1 like) Rattus norvegicus
Analyze
Symbol: Pabpn1l
Name: PABPN1 like
RGD ID: 1562761
Description: Predicted to enable poly(A) binding activity. Predicted to be involved in nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay. Predicted to act upstream of or within maternal-to-zygotic transition of gene expression; negative regulation of SCF-dependent proteasomal ubiquitin-dependent catabolic process; and negative regulation of protein ubiquitination. Predicted to be located in cytoplasm. Predicted to be active in nucleus. Orthologous to human PABPN1L (PABPN1 like, cytoplasmic); PARTICIPATES IN influenza A pathway; mRNA decay pathway; INTERACTS WITH acrylamide; bisphenol A; C60 fullerene.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: Embryonic poly(A)-binding protein 2; Embryonic poly(A)-binding protein type II; embryonic polyadenylate-binding protein 2; ePABP-2; Epabp2; LOC307920; Pabpnl1; poly(A)binding protein nuclear 1-like; poly(A)binding protein nuclear-like 1; RGD1562761; similar to embryonic pol(yA) binding protein 2
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
GRCr81967,578,494 - 67,581,938 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl1967,578,496 - 67,581,895 (-)EnsemblGRCr8
mRatBN7.21950,669,965 - 50,673,409 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1950,669,967 - 50,673,366 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx1957,464,760 - 57,468,206 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01958,144,881 - 58,148,325 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01960,363,378 - 60,366,824 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.01955,430,808 - 55,434,252 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1955,430,810 - 55,434,252 (-)Ensemblrn6Rnor6.0
Rnor_5.01966,139,323 - 66,142,767 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.41952,898,178 - 52,901,622 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera1949,909,361 - 49,912,805 (-)NCBICelera
Cytogenetic Map19q12NCBI
JBrowse:




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

Cellular Component
cytoplasm  (IBA,IEA,ISO)

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. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
4. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:12477932   PMID:15489334  


Genomics

Comparative Map Data
Pabpn1l
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81967,578,494 - 67,581,938 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl1967,578,496 - 67,581,895 (-)EnsemblGRCr8
mRatBN7.21950,669,965 - 50,673,409 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1950,669,967 - 50,673,366 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx1957,464,760 - 57,468,206 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01958,144,881 - 58,148,325 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01960,363,378 - 60,366,824 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.01955,430,808 - 55,434,252 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1955,430,810 - 55,434,252 (-)Ensemblrn6Rnor6.0
Rnor_5.01966,139,323 - 66,142,767 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.41952,898,178 - 52,901,622 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera1949,909,361 - 49,912,805 (-)NCBICelera
Cytogenetic Map19q12NCBI
PABPN1L
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381688,863,333 - 88,870,135 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1688,863,333 - 88,866,660 (-)Ensemblhg38GRCh38
GRCh371688,929,741 - 88,933,068 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361687,455,535 - 87,460,515 (-)NCBIBuild 36Build 36hg18NCBI36
Celera1673,996,625 - 74,001,605 (-)NCBICelera
Cytogenetic Map16q24.3NCBI
HuRef1674,626,902 - 74,630,229 (-)NCBIHuRef
CHM1_11690,341,014 - 90,344,336 (-)NCBICHM1_1
T2T-CHM13v2.01694,933,691 - 94,940,493 (-)NCBIT2T-CHM13v2.0
Pabpn1l
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm398123,346,210 - 123,349,474 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl8123,346,210 - 123,349,478 (-)EnsemblGRCm39 EnsemblGRCm39
GRCm388122,619,471 - 122,622,735 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl8122,619,471 - 122,622,739 (-)Ensemblmm10GRCm38
MGSCv378125,143,371 - 125,146,635 (-)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv368125,505,561 - 125,508,825 (-)NCBIMGSCv36mm8
Celera8126,848,856 - 126,852,111 (-)NCBICelera
Cytogenetic Map8E1NCBI
cM Map871.93NCBI
Pabpn1l
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049555412,718,076 - 2,720,322 (-)Ensembl
ChiLan1.0NW_0049555412,718,076 - 2,720,322 (-)NCBIChiLan1.0ChiLan1.0
PABPN1L
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v21898,638,053 - 98,643,564 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan116104,550,599 - 104,555,722 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01669,579,421 - 69,583,803 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11689,234,156 - 89,237,595 (-)NCBIPanPan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1689,234,156 - 89,237,595 (-)EnsemblpanPan2panpan1.1
PABPN1L
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1564,525,929 - 64,527,654 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha564,537,238 - 64,539,350 (+)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.0564,745,924 - 64,748,036 (+)NCBIROS_Cfam_1.0ROS_Cfam_1.0
UMICH_Zoey_3.1564,772,060 - 64,774,172 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0564,603,706 - 64,605,818 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0565,009,793 - 65,011,905 (+)NCBIUU_Cfam_GSD_1.0UU_Cfam_GSD_1.0
Pabpn1l
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440934925,126,917 - 25,129,241 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_004936641880,548 - 883,098 (+)EnsemblSpeTri2.0 Ensembl
SpeTri2.0NW_004936641880,548 - 883,098 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
PABPN1L
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl6858,888 - 861,604 (+)EnsemblsusScr11Sscrofa11.1
Sscrofa11.16854,605 - 861,969 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.261,049,074 - 1,054,344 (+)NCBISscrofa10.2Sscrofa10.2susScr3
PABPN1L
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1574,251,084 - 74,256,543 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl574,252,703 - 74,255,857 (-)EnsemblChlSab1.1 EnsemblchlSab2Vervet-AGM
Vero_WHO_p1.0NW_0236660471,374,462 - 1,377,258 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Pabpn1l
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_004624746776,677 - 779,555 (+)EnsemblHetGla_female_1.0 EnsemblhetGla2HetGla_female_1.0 Ensembl
HetGla 1.0NW_004624746776,692 - 779,187 (+)NCBIHetGla 1.0HetGla 1.0hetGla2
Pabpn1l
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v11742,247,583 - 42,250,811 (-)NCBIRrattus_CSIRO_v1

miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:54
Count of miRNA genes:49
Interacting mature miRNAs:52
Transcripts:ENSRNOT00000045052
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
631840Niddm38Non-insulin dependent diabetes mellitus QTL 383.86blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)191032907674246245Rat
724546Kidm3Kidney mass QTL 33.1kidney mass (VT:0002707)calculated kidney weight (CMO:0000160)194622677874246245Rat
7411549Bw130Body weight QTL 13050.001body mass (VT:0001259)body weight gain (CMO:0000420)193236531174246245Rat
1331737Uae29Urinary albumin excretion QTL 295.5urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)193628974246245Rat
724518Uae19Urinary albumin excretion QTL 195.5urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)192409397369093973Rat
61423Cia14Collagen induced arthritis QTL 143joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)191083361874246245Rat
2303628Vencon9Ventilatory control QTL 90.005respiration trait (VT:0001943)minute ventilation (CMO:0000132)192318858668188586Rat
2313395Anxrr26Anxiety related response QTL 26aggression-related behavior trait (VT:0015014)tameness/aggressiveness composite score (CMO:0002136)194438513474246245Rat
1578764Stresp19Stress response QTL 193.60.001blood renin amount (VT:0003349)plasma renin activity level (CMO:0000116)193253961574246245Rat
5135224Leukc1Leukocyte quantity QTL 1eosinophil quantity (VT:0002602)blood eosinophil count (CMO:0000033)196124916174246245Rat
1331788Rf45Renal function QTL 452.818kidney blood vessel physiology trait (VT:0100012)absolute change in renal blood flow rate (CMO:0001168)193177788874246245Rat
1554318Bmd5Bone mineral density QTL 512.10.0001lumbar vertebra mineral mass (VT:0010511)volumetric bone mineral density (CMO:0001553)192318858668188586Rat
7247442Uae39Urinary albumin excretion QTL 39urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)19219431774246245Rat
1549835Tcas7Tongue tumor susceptibility QTL 70.001tongue integrity trait (VT:0010553)squamous cell carcinoma of the head and neck tumor number (CMO:0001876)194172254674246245Rat
724566Uae12Urinary albumin excretion QTL 125urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)19219431774246245Rat


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
nervous system
renal system
reproductive system
respiratory system
sensory system
visual system
11 7 50 101 40 41 11 41 11 6 170 109 84 35 50 30 4 4

Sequence


Ensembl Acc Id: ENSRNOT00000045052   ⟹   ENSRNOP00000050572
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl1967,578,496 - 67,581,895 (-)Ensembl
mRatBN7.2 Ensembl1950,669,967 - 50,673,366 (-)Ensembl
Rnor_6.0 Ensembl1955,430,810 - 55,434,252 (-)Ensembl
RefSeq Acc Id: NM_001113779   ⟹   NP_001107251
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81967,578,494 - 67,581,938 (-)NCBI
mRatBN7.21950,669,965 - 50,673,409 (-)NCBI
Rnor_6.01955,430,808 - 55,434,252 (-)NCBI
Rnor_5.01966,139,323 - 66,142,767 (-)NCBI
RGSC_v3.41952,898,178 - 52,901,622 (-)RGD
Celera1949,909,361 - 49,912,805 (-)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_001107251 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAI58790 (Get FASTA)   NCBI Sequence Viewer  
  B0BNE4 (Get FASTA)   NCBI Sequence Viewer  
  EDL92764 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000050572
RefSeq Acc Id: NP_001107251   ⟸   NM_001113779
- UniProtKB: B0BNE4 (UniProtKB/Swiss-Prot),   A0A8L2QPA4 (UniProtKB/TrEMBL),   A6IZT6 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000050572   ⟸   ENSRNOT00000045052
Protein Domains
RRM

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-B0BNE4-F1-model_v2 AlphaFold B0BNE4 1-269 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:1562761 AgrOrtholog
BioCyc Gene G2FUF-5378 BioCyc
Ensembl Genes ENSRNOG00000029558 Ensembl, ENTREZGENE
Ensembl Transcript ENSRNOT00000045052 ENTREZGENE
Gene3D-CATH 3.30.70.330 UniProtKB/Swiss-Prot
IMAGE_CLONE IMAGE:7306904 IMAGE-MGC_LOAD
InterPro Nucleotide-bd_a/b_plait_sf UniProtKB/Swiss-Prot
  RBD_domain_sf UniProtKB/Swiss-Prot
  RRM_dom UniProtKB/Swiss-Prot
KEGG Report rno:307920 UniProtKB/Swiss-Prot
MGC_CLONE MGC:188155 IMAGE-MGC_LOAD
NCBI Gene 307920 ENTREZGENE
PANTHER EMBRYONIC POLYADENYLATE-BINDING PROTEIN 2 UniProtKB/Swiss-Prot
  EUKARYOTIC TRANSLATION INITIATION FACTOR 4B/4H UniProtKB/Swiss-Prot
Pfam RRM_1 UniProtKB/Swiss-Prot
PhenoGen Pabpn1l PhenoGen
PROSITE RRM UniProtKB/Swiss-Prot
RatGTEx ENSRNOG00000029558 RatGTEx
SMART RRM UniProtKB/Swiss-Prot
Superfamily-SCOP SSF54928 UniProtKB/Swiss-Prot
UniProt A0A8L2QPA4 ENTREZGENE, UniProtKB/TrEMBL
  A6IZT6 ENTREZGENE, UniProtKB/TrEMBL
  B0BNE4 ENTREZGENE, UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2021-08-24 Pabpn1l  PABPN1 like  Pabpn1l  poly(A)binding protein nuclear 1-like  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2010-05-21 Pabpn1l  poly(A)binding protein nuclear 1-like  Pabpnl1  poly(A)binding protein nuclear-like 1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-02-29 Pabpnl1  poly(A)binding protein nuclear-like 1  RGD1562761_predicted  similar to embryonic pol(yA) binding protein 2 (predicted)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-03-07 RGD1562761_predicted  similar to embryonic pol(yA) binding protein 2 (predicted)  LOC307920  similar to embryonic pol(yA) binding protein 2  Symbol and Name status set to approved 1299863 APPROVED
2006-02-09 LOC307920  similar to embryonic pol(yA) binding protein 2      Symbol and Name status set to provisional 70820 PROVISIONAL