Human Gene PABPN1L (uc010vpe.2) Description and Page Index
  Description: Homo sapiens poly(A) binding protein, nuclear 1-like (cytoplasmic) (PABPN1L), mRNA.
Transcript (Including UTRs)
   Position: hg19 chr16:88,929,748-88,933,068 Size: 3,321 Total Exon Count: 7 Strand: -
Coding Region
   Position: hg19 chr16:88,930,164-88,933,014 Size: 2,851 Coding Exon Count: 7 

Page IndexSequence and LinksUniProtKB CommentsCTDGene AllelesRNA-Seq Expression
Microarray ExpressionRNA StructureProtein StructureOther SpeciesGO AnnotationsmRNA Descriptions
Other NamesModel InformationMethods
Data last updated: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr16:88,929,748-88,933,068)mRNA (may differ from genome)Protein (278 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaBioGPS
CGAPEnsemblEntrez GeneExonPrimerGeneCardsHGNC
HPRDLynxMGIneXtProtPubMedStanford SOURCE
UniProtKB

-  Comments and Description Text from UniProtKB
  ID: EPAB2_HUMAN
DESCRIPTION: RecName: Full=Embryonic polyadenylate-binding protein 2; Short=Embryonic poly(A)-binding protein 2; Short=ePABP-2; Short=ePABP2; AltName: Full=Embryonic poly(A)-binding protein type II; AltName: Full=Poly(A)-binding protein nuclear-like 1;
FUNCTION: Binds the poly(A) tail of mRNA (By similarity).
SUBCELLULAR LOCATION: Cytoplasm (By similarity).
TISSUE SPECIFICITY: Expressed in various adult tissues.
SIMILARITY: Contains 1 RRM (RNA recognition motif) domain.

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene

+  Common Gene Haplotype Alleles
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-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 1.52 RPKM in Brain - Cerebellum
Total median expression: 7.19 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
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-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -33.6054-0.622 Picture PostScript Text
3' UTR -186.00416-0.447 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR012677 - Nucleotide-bd_a/b_plait
IPR000504 - RRM_dom

Pfam Domains:
PF00076 - RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain)

SCOP Domains:
54928 - RNA-binding domain, RBD

ModBase Predicted Comparative 3D Structure on A6NDY0
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The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologGenome BrowserNo orthologNo orthologNo orthologGenome Browser
Gene DetailsGene Details   Gene Details
Gene SorterGene Sorter   Gene Sorter
 RGD   SGD
 Protein Sequence   Protein Sequence
 Alignment   Alignment

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0003676 nucleic acid binding
GO:0003723 RNA binding

Cellular Component:
GO:0005737 cytoplasm


-  Descriptions from all associated GenBank mRNAs
  BC148673 - Synthetic construct Homo sapiens clone IMAGE:100015599, MGC:183118 similar to poly(A)binding protein nuclear-like 1 (LOC390748) mRNA, encodes complete protein.
BC156595 - Synthetic construct Homo sapiens clone IMAGE:100062070, MGC:190159 similar to poly(A)binding protein nuclear-like 1 (LOC390748) mRNA, encodes complete protein.
AB528852 - Synthetic construct DNA, clone: pF1KE0573, Homo sapiens PABPNL1 gene for Embryonic polyadenylate-binding protein 2, without stop codon, in Flexi system.
EU190484 - Homo sapiens ePABP2 mRNA, complete cds.
BC130001 - Homo sapiens similar to poly(A)binding protein nuclear-like 1, mRNA (cDNA clone MGC:157954 IMAGE:40133435), complete cds.
BC130002 - Homo sapiens similar to poly(A)binding protein nuclear-like 1, mRNA (cDNA clone IMAGE:40133437), partial cds.

-  Other Names for This Gene
  Alternate Gene Symbols: A1L3B3, A2VDI2, A6NDY0, EPAB2_HUMAN, EPABP2, NM_001080487, NP_001073956, PABPNL1
UCSC ID: uc010vpe.2
RefSeq Accession: NM_001080487
Protein: A6NDY0 (aka EPAB2_HUMAN)
CCDS: CCDS45547.2

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_001080487.2
exon count: 7CDS single in 3' UTR: no RNA size: 1309
ORF size: 837CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 1682.00frame shift in genome: no % Coverage: 99.85
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 0# strange splices: 0
Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.