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

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Gene: Pabpc1l (poly(A) binding protein, cytoplasmic 1-like) Mus musculus
Analyze
Symbol: Pabpc1l
Name: poly(A) binding protein, cytoplasmic 1-like
RGD ID: 1612607
MGI Page MGI
Description: Predicted to enable mRNA 3'-UTR binding activity; poly(A) binding activity; and poly(U) RNA binding activity. Acts upstream of or within RNA metabolic process; nucleus localization; and oocyte maturation. Predicted to be part of ribonucleoprotein complex. Predicted to be active in cytoplasmic stress granule; cytosol; and nucleus. Is expressed in early conceptus and gonad. Orthologous to human PABPC1L (poly(A) binding protein cytoplasmic 1 like).
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: 1810053B01Rik; embryonic poly(A)-binding protein; eP; Epab; polyadenylate-binding protein 1-like
RGD Orthologs
Human
Rat
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: GRCm39 - Mouse Genome Assembly GRCm39
Position:
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm392163,866,685 - 163,892,458 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl2163,867,370 - 163,892,458 (+)EnsemblGRCm39 Ensembl
GRCm382164,024,770 - 164,050,538 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl2164,025,450 - 164,050,538 (+)EnsemblGRCm38mm10GRCm38
MGSCv372163,851,186 - 163,876,274 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv362163,716,922 - 163,741,480 (+)NCBIMGSCv36mm8
Celera2169,955,661 - 169,980,596 (+)NCBICelera
Cytogenetic Map2H3NCBI
cM Map284.6NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
# Reference Title Reference Citation
1. KEGG Annotation Import Pipeline Pipeline to import KEGG annotations from KEGG into RGD
2. Mouse MP Annotation Import Pipeline RGD automated import pipeline
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:8889548   PMID:10349636   PMID:11042159   PMID:11076861   PMID:11217851   PMID:12466851   PMID:12477932   PMID:14610273   PMID:15475267   PMID:15630085   PMID:16141072   PMID:16141073  
PMID:21267068   PMID:21677750   PMID:21873635   PMID:22621333   PMID:22814100   PMID:24599567   PMID:25034140   PMID:25370180   PMID:26134869   PMID:26492470   PMID:28203794   PMID:30302808  
PMID:30973865   PMID:31598710   PMID:34972250   PMID:36823316   PMID:37052235  


Genomics

Comparative Map Data
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 Ensembl
GRCm382164,024,770 - 164,050,538 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl2164,025,450 - 164,050,538 (+)EnsemblGRCm38mm10GRCm38
MGSCv372163,851,186 - 163,876,274 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv362163,716,922 - 163,741,480 (+)NCBIMGSCv36mm8
Celera2169,955,661 - 169,980,596 (+)NCBICelera
Cytogenetic Map2H3NCBI
cM Map284.6NCBI
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 (+)EnsemblGRCh38hg38GRCh38
GRCh372043,538,701 - 43,567,957 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 362042,972,117 - 43,001,376 (+)NCBINCBI36Build 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
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr83173,111,856 - 173,145,389 (+)NCBIGRCr8
mRatBN7.23152,692,825 - 152,725,997 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl3152,693,700 - 152,725,997 (+)EnsemblmRatBN7.2 Ensembl
Rnor_6.03160,410,733 - 160,447,073 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl3160,410,757 - 160,444,940 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.03166,597,627 - 166,629,983 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.43154,959,889 - 154,992,338 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera3151,342,191 - 151,376,854 (+)NCBICelera
Cytogenetic Map3q42NCBI
Pabpc1l
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495544512,422,204 - 12,450,024 (-)EnsemblChiLan1.0
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 (+)Ensemblpanpan1.1panPan2
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 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2431,973,114 - 31,994,462 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.02433,038,733 - 33,059,922 (+)NCBIROS_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_1.0
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 (-)EnsemblSpeTri2.0SpeTri2.0 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 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
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 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
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_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046247909,545,719 - 9,572,447 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Pabpc1l
1072 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:729
Count of miRNA genes:483
Interacting mature miRNAs:557
Transcripts:ENSMUST00000067715, ENSMUST00000126272, ENSMUST00000141671, ENSMUST00000150523, ENSMUST00000156087
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 (GRCm39)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
5491196Mobq6_mmultigenic obesity QTL 6 (mouse)Not determined285724269180896594Mouse
11038702Ltpr2_mLeishmania tropica response 2 (mouse)2103095716167212356Mouse
1301618Bglu1_mblood glucose level 1 (mouse)Not determined2117942930174324863Mouse
27226749Femd10_mfemur midshaft diameter 10, 16 week (mouse)2124441920168241920Mouse
1301961Bts1_mbladder tumor susceptibility 1 (mouse)Not determined2132024159166024330Mouse
11049567Lmr28f_mleishmaniasis resistance 28f (mouse)2133144911167145058Mouse
11049566Lmr28e_mleishmaniasis resistance 28e (mouse)2133144911167145058Mouse
11341717Rvfs1_mRift Valley fever susceptibility 1 (mouse)2135432544173449616Mouse
4141703Chlq13_mcirculating hormone level QTL 13 (mouse)Not determined2135699221169699361Mouse
1301907Rends_mrenal disease susceptibility (mouse)Not determined2135699221169699361Mouse
10043956Gnf5_mgrowth and fatness 5 (mouse)Not determined2135699221169699361Mouse
10054066Bwq9_mbody weight QTL 9 (mouse)Not determined2135699221169699361Mouse
1300846Pbwg11_mpostnatal body weight growth 11 (mouse)Not determined2138966600172966729Mouse
11353826Bdln10_mbody length 10 (mouse)2140441482174441482Mouse
12801461Intim1_mintima modifier 1 (mouse)2142428347176428450Mouse
12801456Intmrm1_mintima/media ratio modifier 1 (mouse)2142428347176428450Mouse
1301783Bhr1_mbronchial hyperresponsiveness 1 (mouse)Not determined2142593476178442452Mouse
1357484Bsbob_mBSB obesity (mouse)Not determined2143773445165665019Mouse
1558939Gnf1_mgrowth and fatness 1 (mouse)Not determined2143773445169117924Mouse
1300867Lore2_mloss of righting induced by ethanol 2 (mouse)Not determined2144515861180896594Mouse
1302013Tbbmd3_mtotal body bone mineral density 3 (mouse)Not determined2145196949179197085Mouse
1300806Aod4_mautoimmune ovarian dysgenesis 4 (mouse)Not determined2145228719179228841Mouse
1301865Hdlq19_mHDL QTL 19 (mouse)Not determined2145518775179518926Mouse
12790983Bwq12_mbody weight QTL 12 (mouse)2148238204181755017Mouse
4142211Nilac3_mnicotine induced locomotor activity 3 (mouse)Not determined2148664893181755017Mouse
1558917Gct8_mgranulosa cell tumorigenesis 8 (mouse)Not determined2149236907181755017Mouse
1300751Bdt1_mbone density traits 1 (mouse)Not determined2149988902181755017Mouse
1301085Lrnx10_mlearning-contextual 10 (mouse)Not determined2150212221181755017Mouse
11038701Ltpr2e_mLeishmania tropica response 2e (mouse)2150212221181755017Mouse
4142450Lmr16_mleishmaniasis resistance 16 (mouse)Not determined2150212221181755017Mouse
10412080Hylaq2_mHyperlocomotor activity related QTL 2 (mouse)Not determined2151640941164119146Mouse
12910520Scgq3_mspontaneous crescentic glomerulonephritis QTL 3 (mouse)2151709273174389124Mouse
1301019Bmd6_mbone mineral density 6 (mouse)Not determined2151778297181755017Mouse
14747002Mancz3_mmandible centroid size 3 (mouse)2152329820181755017Mouse
1558867Gnf3_mgrowth and fatness 3 (mouse)Not determined2152699221169117924Mouse
1300622Cfld1_mcystic fibrosis lung disease 1 (mouse)Not determined2155823920181755017Mouse
1357537Lith12_mlithogenic gene 12 (mouse)Not determined2156196464181755017Mouse
1300688Nidd2k_mNidd2 on KK-A (mouse)Not determined2158078337178442452Mouse
12910800Pwgrq3_mpre-weaning growth rate QTL 3 (mouse)2160611165169794802Mouse
12910810Pwbwq2_mpre-weaning body weight QTL 2 (mouse)2160611165169794802Mouse
1302003Sluc17_msusceptibility to lung cancer 17 (mouse)Not determined2162433493181755017Mouse
1558991Tailq4_mtail length QTL 4 (mouse)Not determined2162736926178442452Mouse
1357435Epfq2_mepididymal fat pad weight QTL 2 (mouse)Not determined2162736926178442452Mouse
1301677Alcp6_malcohol preference locus 6 (mouse)Not determined2163486407181755017Mouse
1301348Alcp5_malcohol preference locus 5 (mouse)Not determined2163486407181755017Mouse

Markers in Region
1810053B01Rik  
Mouse AssemblyChrPosition (strand)SourceJBrowse
cM Map2 UniSTS
cM Map2 UniSTS
D20S528E  
Mouse AssemblyChrPosition (strand)SourceJBrowse
GRCm3846,354,006 - 6,354,128UniSTSGRCm38
GRCm382164,018,311 - 164,018,439UniSTSGRCm38
MGSCv3746,281,153 - 6,281,275UniSTSGRCm37
MGSCv372163,844,047 - 163,844,175UniSTSGRCm37
Celera46,272,288 - 6,272,410UniSTS
Celera2169,948,527 - 169,948,651UniSTS
Cytogenetic Map2H3UniSTS
1810053B01Rik  
Mouse AssemblyChrPosition (strand)SourceJBrowse
Cytogenetic Map2H3UniSTS
cM Map2 UniSTS
1810053B01Rik  
Mouse AssemblyChrPosition (strand)SourceJBrowse
Cytogenetic Map2H3UniSTS


Expression


Sequence


RefSeq Acc Id: ENSMUST00000067715   ⟹   ENSMUSP00000096701
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl2163,867,370 - 163,892,458 (+)Ensembl
GRCm38.p6 Ensembl2164,025,450 - 164,050,538 (+)Ensembl
RefSeq Acc Id: ENSMUST00000126272
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl2163,889,307 - 163,892,458 (+)Ensembl
GRCm38.p6 Ensembl2164,047,387 - 164,050,538 (+)Ensembl
RefSeq Acc Id: ENSMUST00000141671
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl2163,873,091 - 163,884,240 (+)Ensembl
GRCm38.p6 Ensembl2164,031,171 - 164,042,320 (+)Ensembl
RefSeq Acc Id: ENSMUST00000150523
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl2163,889,930 - 163,892,087 (+)Ensembl
GRCm38.p6 Ensembl2164,048,010 - 164,050,167 (+)Ensembl
RefSeq Acc Id: ENSMUST00000156087
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl2163,878,920 - 163,884,467 (+)Ensembl
GRCm38.p6 Ensembl2164,037,000 - 164,042,547 (+)Ensembl
RefSeq Acc Id: NM_001114079   ⟹   NP_001107551
RefSeq Status: VALIDATED
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm392163,867,144 - 163,892,458 (+)NCBI
GRCm382164,025,224 - 164,050,538 (+)NCBI
MGSCv372163,851,186 - 163,876,274 (+)RGD
Celera2169,955,435 - 169,980,596 (+)NCBI
cM Map2 ENTREZGENE
Sequence:
RefSeq Acc Id: XM_006499829   ⟹   XP_006499892
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm392163,866,685 - 163,884,405 (+)NCBI
GRCm382164,024,770 - 164,042,482 (+)NCBI
Sequence:
RefSeq Acc Id: XM_036162344   ⟹   XP_036018237
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm392163,869,511 - 163,892,458 (+)NCBI
Sequence:
Protein Sequences
Protein RefSeqs NP_001107551 (Get FASTA)   NCBI Sequence Viewer  
  XP_006499892 (Get FASTA)   NCBI Sequence Viewer  
  XP_036018237 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAI58031 (Get FASTA)   NCBI Sequence Viewer  
  ACD43645 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSMUSP00000096701
  ENSMUSP00000096701.4
RefSeq Acc Id: NP_001107551   ⟸   NM_001114079
- UniProtKB: A2A5N3 (UniProtKB/TrEMBL),   B2RXY9 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006499892   ⟸   XM_006499829
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: ENSMUSP00000096701   ⟸   ENSMUST00000067715
RefSeq Acc Id: XP_036018237   ⟸   XM_036162344
- Peptide Label: isoform X1
Protein Domains
PABC   RRM

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-A2A5N3-F1-model_v2 AlphaFold A2A5N3 1-607 view protein structure

Promoters
RGD ID:6831995
Promoter ID:MM_KWN:32883
Type:CpG-Island
SO ACC ID:SO:0000170
Source:MPROMDB
Tissues & Cell Lines:BoneMarrow_0Hour,   BoneMarrow_4Hour
Transcripts:NM_001114079
Position:
Mouse AssemblyChrPosition (strand)Source
MGSCv362163,850,901 - 163,851,401 (+)MPROMDB
RGD ID:6879602
Promoter ID:EPDNEW_M3252
Type:initiation region
Name:Pabpc1l_1
Description:Mus musculus poly binding protein, cytoplasmic 1-like , mRNA.
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm382164,047,387 - 164,047,447EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene MGI:1922908 AgrOrtholog
Ensembl Genes ENSMUSG00000054582 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSMUST00000067715 ENTREZGENE
  ENSMUST00000067715.5 UniProtKB/TrEMBL
Gene3D-CATH 3.30.70.330 UniProtKB/TrEMBL
  c-terminal domain of poly(a) binding protein UniProtKB/TrEMBL
InterPro 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 UniProtKB/TrEMBL
  RRM_dom_euk UniProtKB/TrEMBL
KEGG Report mmu:381404 UniProtKB/TrEMBL
MGD MGI:1922908 ENTREZGENE
NCBI Gene 381404 ENTREZGENE
PANTHER POLYADENYLATE-BINDING PROTEIN 1-LIKE UniProtKB/TrEMBL
  RNA BINDING PROTEIN UniProtKB/TrEMBL
Pfam PABP UniProtKB/TrEMBL
  RRM_1 UniProtKB/TrEMBL
PhenoGen Pabpc1l PhenoGen
PROSITE PABC UniProtKB/TrEMBL
  RRM UniProtKB/TrEMBL
SMART PolyA UniProtKB/TrEMBL
  RRM UniProtKB/TrEMBL
  RRM_1 UniProtKB/TrEMBL
Superfamily-SCOP PABP_HYD UniProtKB/TrEMBL
  SSF54928 UniProtKB/TrEMBL
UniProt A2A5N3 ENTREZGENE, UniProtKB/TrEMBL
  B2RXY9 ENTREZGENE, UniProtKB/TrEMBL