Human Gene NPIPB13 (uc010vem.2)
  Description: Homo sapiens nuclear pore complex interacting protein pseudogene (NPIPB13), non-coding RNA.
Transcript (Including UTRs)
   Position: hg19 chr16:30,234,350-30,257,122 Size: 22,773 Total Exon Count: 8 Strand: -
Coding Region
   Position: hg19 chr16:30,234,350-30,256,894 Size: 22,545 Coding Exon Count: 7 

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

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr16:30,234,350-30,257,122)mRNA (may differ from genome)Protein (1138 aa)
Gene SorterGenome BrowserOther Species FASTATable SchemaAlphaFoldBioGPS
EnsemblExonPrimerGeneCardsGeneNetworkH-INVLynx
MGIneXtProtPubMedUniProtKB

-  Comments and Description Text from UniProtKB
  ID: YP038_HUMAN
DESCRIPTION: RecName: Full=Putative NPIP-like protein LOC613037;
SUBCELLULAR LOCATION: Membrane; Single-pass membrane protein (Potential).
SIMILARITY: Belongs to the NPIP family.
CAUTION: Could be the product of a pseudogene.

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 1.97 RPKM in Thyroid
Total median expression: 46.11 RPKM



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

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -17.7075-0.236 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
IPR009443 - NPIP

Pfam Domains:
PF06409 - Nuclear pore complex interacting protein (NPIP)

ModBase Predicted Comparative 3D Structure on A6NJU9
FrontTopSide
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 orthologNo orthologNo orthologNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
      
      
      

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Cellular Component:
GO:0005654 nucleoplasm
GO:0016020 membrane
GO:0016021 integral component of membrane


-  Descriptions from all associated GenBank mRNAs
  AK300277 - Homo sapiens cDNA FLJ56869 complete cds.
AK301703 - Homo sapiens cDNA FLJ56875 complete cds.
AK296301 - Homo sapiens cDNA FLJ56878 complete cds.
AK295170 - Homo sapiens cDNA FLJ54462 complete cds.
AK303607 - Homo sapiens cDNA FLJ61625 complete cds.
AK128772 - Homo sapiens cDNA FLJ45371 fis, clone BRHIP3017855, highly similar to Homo sapiens nuclear pore complex interacting protein (NPIP).
JD041122 - Sequence 22146 from Patent EP1572962.
CU690320 - Synthetic construct Homo sapiens gateway clone IMAGE:100018410 5' read LOC23117 mRNA.
JD347493 - Sequence 328517 from Patent EP1572962.
JD347493 - Sequence 328517 from Patent EP1572962.
JD148745 - Sequence 129769 from Patent EP1572962.
KF175184 - Homo sapiens clone 20 nuclear pore complex-interacting protein (NPIP) mRNA, partial cds.
KF175178 - Homo sapiens clone 14 nuclear pore complex-interacting protein (NPIP) mRNA, partial cds.
KF175193 - Homo sapiens clone 29 nuclear pore complex-interacting protein (NPIP) mRNA, partial cds.
KF175194 - Homo sapiens clone 30 nuclear pore complex-interacting protein (NPIP) mRNA, partial cds.
KF175179 - Homo sapiens clone 15 nuclear pore complex-interacting protein (NPIP) mRNA, partial cds.
KF175180 - Homo sapiens clone 16 nuclear pore complex-interacting protein (NPIP) mRNA, partial cds.
KF175182 - Homo sapiens clone 18 nuclear pore complex-interacting protein (NPIP) mRNA, partial cds.
KF175185 - Homo sapiens clone 21 nuclear pore complex-interacting protein (NPIP) mRNA, partial cds.
KF175186 - Homo sapiens clone 22 nuclear pore complex-interacting protein (NPIP) mRNA, partial cds.
KF175187 - Homo sapiens clone 23 nuclear pore complex-interacting protein (NPIP) mRNA, partial cds.
KF175190 - Homo sapiens clone 26 nuclear pore complex-interacting protein (NPIP) mRNA, partial cds.
KF175201 - Homo sapiens clone 37 nuclear pore complex-interacting protein (NPIP) mRNA, partial cds.
KF175188 - Homo sapiens clone 24 nuclear pore complex-interacting protein (NPIP) mRNA, partial cds.
KF175189 - Homo sapiens clone 25 nuclear pore complex-interacting protein (NPIP) mRNA, partial cds.
KF175191 - Homo sapiens clone 27 nuclear pore complex-interacting protein (NPIP) mRNA, partial cds.
KF175192 - Homo sapiens clone 28 nuclear pore complex-interacting protein (NPIP) mRNA, partial cds.
KF175195 - Homo sapiens clone 31 nuclear pore complex-interacting protein (NPIP) mRNA, partial cds.
KF175196 - Homo sapiens clone 32 nuclear pore complex-interacting protein (NPIP) mRNA, partial cds.
KF175197 - Homo sapiens clone 33 nuclear pore complex-interacting protein (NPIP) mRNA, partial cds.
KF175202 - Homo sapiens clone 38 nuclear pore complex-interacting protein (NPIP) mRNA, partial cds.
KF175218 - Homo sapiens clone p_11 nuclear pore complex-interacting protein (NPIP) pseudogene mRNA, partial sequence.
KF175216 - Homo sapiens clone p_9 nuclear pore complex-interacting protein (NPIP) pseudogene mRNA, partial sequence.
KF175198 - Homo sapiens clone 34 nuclear pore complex-interacting protein (NPIP) mRNA, partial cds.
KF175199 - Homo sapiens clone 35 nuclear pore complex-interacting protein (NPIP) mRNA, partial cds.
KF175200 - Homo sapiens clone 36 nuclear pore complex-interacting protein (NPIP) mRNA, partial cds.
KF175203 - Homo sapiens clone 39 nuclear pore complex-interacting protein (NPIP) mRNA, partial cds.
KF175205 - Homo sapiens clone 41 nuclear pore complex-interacting protein (NPIP) mRNA, partial cds.
KF175206 - Homo sapiens clone 42 nuclear pore complex-interacting protein (NPIP) mRNA, partial cds.
KF175215 - Homo sapiens clone p_8 nuclear pore complex-interacting protein (NPIP) pseudogene mRNA, partial sequence.
JD318007 - Sequence 299031 from Patent EP1572962.
KF175181 - Homo sapiens clone 17 nuclear pore complex-interacting protein (NPIP) mRNA, partial cds.
AK308629 - Homo sapiens cDNA, FLJ98670.
KF175183 - Homo sapiens clone 19 nuclear pore complex-interacting protein (NPIP) mRNA, partial cds.
DQ597666 - Homo sapiens piRNA piR-35732, complete sequence.
DQ586845 - Homo sapiens piRNA piR-53957, complete sequence.
JD444458 - Sequence 425482 from Patent EP1572962.
JD374720 - Sequence 355744 from Patent EP1572962.
JD488661 - Sequence 469685 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: A6NJU9, AK295170, LOC613037, YP038_HUMAN
UCSC ID: uc010vem.2
RefSeq Accession: NR_002555
Protein: A6NJU9 (aka YP038_HUMAN)

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: AK295170.1
exon count: 8CDS single in 3' UTR: no RNA size: 3695
ORF size: 3417CDS single in intron: no Alignment % ID: 99.62
txCdsPredict score: 3592.00frame shift in genome: no % Coverage: 59.03
has start codon: yes stop codon in genome: no # of Alignments: 2
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.