Human Gene NPIPA1 (ENST00000328085.10) from GENCODE V44
  Description: Homo sapiens nuclear pore complex interacting protein family member A1 (NPIPA1), mRNA. (from RefSeq NM_006985)
Gencode Transcript: ENST00000328085.10
Gencode Gene: ENSG00000183426.17
Transcript (Including UTRs)
   Position: hg38 chr16:14,937,443-14,952,056 Size: 14,614 Total Exon Count: 8 Strand: +
Coding Region
   Position: hg38 chr16:14,937,443-14,952,025 Size: 14,583 Coding Exon Count: 8 

Page IndexSequence and LinksUniProtKB CommentsPrimersRNA-Seq ExpressionMicroarray Expression
RNA StructureProtein StructureOther SpeciesGO AnnotationsmRNA DescriptionsOther Names
Methods
Data last updated at UCSC: 2023-08-18 00:09:47

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr16:14,937,443-14,952,056)mRNA (may differ from genome)Protein (350 aa)
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PubMedUniProtKBBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: NPIP_HUMAN
DESCRIPTION: RecName: Full=Nuclear pore complex-interacting protein; Short=NPIP;
SUBUNIT: May associate with the nuclear pore complex.
SUBCELLULAR LOCATION: Nucleus, nuclear pore complex. Nucleus membrane. Note=Colocalizes with nuclear pore complex protein NUP62.
TISSUE SPECIFICITY: Widely expressed.
SIMILARITY: Belongs to the NPIP family.

-  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


-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 79.95 RPKM in Brain - Cerebellum
Total median expression: 772.95 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
3' UTR 0.00310.000 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 Q9UND3
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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 orthologNo orthologNo orthologNo orthologNo orthologNo ortholog
      
      
      
      
      

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Biological Process:
GO:0015031 protein transport
GO:0051028 mRNA transport

Cellular Component:
GO:0005634 nucleus
GO:0005643 nuclear pore
GO:0005654 nucleoplasm
GO:0016020 membrane
GO:0031965 nuclear membrane


-  Descriptions from all associated GenBank mRNAs
  KJ906490 - Synthetic construct Homo sapiens clone ccsbBroadEn_16160 PKD1P1 gene, encodes complete protein.
AB209632 - Homo sapiens mRNA for PI-3-kinase-related kinase SMG-1 isoform 1homolog protein.
AK316459 - Homo sapiens cDNA, FLJ79358 complete cds.
AK303607 - Homo sapiens cDNA FLJ61625 complete cds.
AK293635 - Homo sapiens cDNA FLJ59829 complete cds.
AK296301 - Homo sapiens cDNA FLJ56878 complete cds.
AK310414 - Homo sapiens cDNA, FLJ17456.
AK160377 - Homo sapiens mRNA for FLJ00322 protein.
BC023572 - Homo sapiens mRNA similar to polycystic kidney disease 1 (autosomal dominant) (cDNA clone IMAGE:4559025).
BC063821 - Homo sapiens cDNA clone IMAGE:6192147, **** WARNING: chimeric clone ****.
KF175209 - Homo sapiens clone p_2 nuclear pore complex-interacting protein (NPIP) pseudogene mRNA, partial sequence.
KF175211 - Homo sapiens clone p_4 nuclear pore complex-interacting protein (NPIP) pseudogene mRNA, partial sequence.
KF175212 - Homo sapiens clone p_5 nuclear pore complex-interacting protein (NPIP) pseudogene mRNA, partial sequence.
KF175214 - Homo sapiens clone p_7 nuclear pore complex-interacting protein (NPIP) pseudogene mRNA, partial sequence.
KF175219 - Homo sapiens clone p_12 nuclear pore complex-interacting protein (NPIP) pseudogene mRNA, partial sequence.
KF175165 - Homo sapiens clone 1 nuclear pore complex-interacting protein (NPIP) mRNA, partial cds.
KF175166 - Homo sapiens clone 2 nuclear pore complex-interacting protein (NPIP) mRNA, partial cds.
KF175167 - Homo sapiens clone 3 nuclear pore complex-interacting protein (NPIP) mRNA, partial cds.
KF175174 - Homo sapiens clone 10 nuclear pore complex-interacting protein (NPIP) mRNA, partial cds.
KF175213 - Homo sapiens clone p_6 nuclear pore complex-interacting protein (NPIP) pseudogene mRNA, partial sequence.
CU692310 - Synthetic construct Homo sapiens gateway clone IMAGE:100021387 5' read LOC339047 mRNA.
AB528194 - Synthetic construct DNA, clone: pF1KB7383, Homo sapiens NPIP gene for nuclear pore complex interacting protein, without stop codon, in Flexi system.
KF175225 - Homo sapiens clone K2.5 nuclear pore complex-interacting protein A type (NPIPA) mRNA, complete cds.
BC146422 - Synthetic construct Homo sapiens clone IMAGE:100015091, MGC:180199 nuclear pore complex interacting protein (NPIP) mRNA, encodes complete protein.
AF132984 - Homo sapiens nuclear pore complex interacting protein NPIP (NPIP) mRNA, complete cds.
KF175169 - Homo sapiens clone 5 nuclear pore complex-interacting protein (NPIP) mRNA, partial cds.
KF175172 - Homo sapiens clone 8 nuclear pore complex-interacting protein (NPIP) mRNA, partial cds.
KF175170 - Homo sapiens clone 6 nuclear pore complex-interacting protein (NPIP) mRNA, partial cds.
KF175208 - Homo sapiens clone p_1 nuclear pore complex-interacting protein (NPIP) pseudogene mRNA, partial sequence.
KF175210 - Homo sapiens clone p_3 nuclear pore complex-interacting protein (NPIP) pseudogene mRNA, partial sequence.
KF175168 - Homo sapiens clone 4 nuclear pore complex-interacting protein (NPIP) mRNA, partial cds.
KF175171 - Homo sapiens clone 7 nuclear pore complex-interacting protein (NPIP) mRNA, partial cds.
AB075516 - Homo sapiens neuroblastoma cDNA, clone:Nbla00537, full insert sequence.
JD462309 - Sequence 443333 from Patent EP1572962.
JD510674 - Sequence 491698 from Patent EP1572962.
KF175173 - Homo sapiens clone 9 nuclear pore complex-interacting protein (NPIP) mRNA, partial cds.
DQ586845 - Homo sapiens piRNA piR-53957, complete sequence.
JD047111 - Sequence 28135 from Patent EP1572962.
AK294177 - Homo sapiens cDNA FLJ56769 complete cds, weakly similar to Nuclear pore complex-interacting protein.
JD318007 - Sequence 299031 from Patent EP1572962.
JD148746 - Sequence 129770 from Patent EP1572962.
JD347493 - Sequence 328517 from Patent EP1572962.
JD391234 - Sequence 372258 from Patent EP1572962.
JD082959 - Sequence 63983 from Patent EP1572962.
JD347493 - Sequence 328517 from Patent EP1572962.
JD143063 - Sequence 124087 from Patent EP1572962.
JD416161 - Sequence 397185 from Patent EP1572962.
JD082959 - Sequence 63983 from Patent EP1572962.
JD347493 - Sequence 328517 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: ENST00000328085.1, ENST00000328085.2, ENST00000328085.3, ENST00000328085.4, ENST00000328085.5, ENST00000328085.6, ENST00000328085.7, ENST00000328085.8, ENST00000328085.9, NM_006985, NPIP, NPIP_HUMAN, O15102, Q9UND3, uc002dcy.1, uc002dcy.2, uc002dcy.3, uc002dcy.4, uc002dcy.5
UCSC ID: ENST00000328085.10
RefSeq Accession: NM_006985
Protein: Q9UND3 (aka NPIP_HUMAN)
CCDS: CCDS10557.1

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