Human Gene PABPN1L (uc002fmj.3) 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: 6 Strand: -
Coding Region
   Position: hg19 chr16:88,930,000-88,933,014 Size: 3,015 Coding Exon Count: 6 

Page IndexSequence and LinksUniProtKB CommentsCTDGene AllelesRNA-Seq Expression
Microarray ExpressionRNA StructureProtein StructureOther SpeciesmRNA DescriptionsOther Names
Model 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 (297 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaBioGPS
MGIPubMedStanford SOURCEUniProtKB

-  Comments and Description Text from UniProtKB
DESCRIPTION: SubName: Full=Embryonic polyadenylate-binding protein 2;
CAUTION: The sequence shown here is derived from an Ensembl automatic analysis pipeline and should be considered as preliminary data.

-  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 -95.50252-0.379 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
  ModBase Predicted Comparative 3D Structure on C9JEK9
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 orthologNo ortholog
Gene DetailsGene Details    
Gene SorterGene Sorter    
 Protein Sequence    

-  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: BC130002, C9JEK9, C9JEK9_HUMAN
UCSC ID: uc002fmj.3
RefSeq Accession: NM_001080487
Protein: C9JEK9

-  Gene Model Information
category: coding nonsense-mediated-decay: no RNA accession: BC130002.1
exon count: 6CDS single in 3' UTR: no RNA size: 856
ORF size: 894CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 1632.00frame shift in genome: no % Coverage: 99.77
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.