Human Gene NIPSNAP2 (ENST00000322090.8_4) from GENCODE V47lift37
  Description: nipsnap homolog 2, transcript variant 1 (from RefSeq NM_001483.3)
Gencode Transcript: ENST00000322090.8_4
Gencode Gene: ENSG00000146729.10_12
Transcript (Including UTRs)
   Position: hg19 chr7:56,032,278-56,067,872 Size: 35,595 Total Exon Count: 10 Strand: +
Coding Region
   Position: hg19 chr7:56,032,303-56,066,765 Size: 34,463 Coding Exon Count: 10 

Page IndexSequence and LinksUniProtKB CommentsPrimersGene AllelesRNA-Seq Expression
Microarray ExpressionRNA StructureProtein StructureOther SpeciesGO AnnotationsmRNA Descriptions
Other NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr7:56,032,278-56,067,872)mRNA (may differ from genome)Protein (286 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGeneCardsMGI
OMIMPubMedUniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: NIPS2_HUMAN
DESCRIPTION: RecName: Full=Protein NipSnap homolog 2; Short=NipSnap2; AltName: Full=Glioblastoma-amplified sequence;
INTERACTION: O95166:GABARAP; NbExp=5; IntAct=EBI-307133, EBI-712001; Q9H0R8:GABARAPL1; NbExp=6; IntAct=EBI-307133, EBI-746969; P60520:GABARAPL2; NbExp=4; IntAct=EBI-307133, EBI-720116; Q9GZQ8:MAP1LC3B; NbExp=4; IntAct=EBI-307133, EBI-373144; Q9BXW4:MAP1LC3C; NbExp=2; IntAct=EBI-307133, EBI-2603996;
TISSUE SPECIFICITY: Widely expressed. Most abundant in heart and skeletal muscle.
SIMILARITY: Belongs to the NipSnap 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


+  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: 120.11 RPKM in Muscle - Skeletal
Total median expression: 1352.06 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 -7.8025-0.312 Picture PostScript Text
3' UTR -239.501107-0.216 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
IPR011008 - Dimeric_a/b-barrel
IPR012577 - NIPSNAP

Pfam Domains:
PF07978 - NIPSNAP

SCOP Domains:
54909 - Dimeric alpha+beta barrel

ModBase Predicted Comparative 3D Structure on O75323
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 DetailsGene Details    
Gene SorterGene Sorter    
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-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005515 protein binding

Biological Process:
GO:0006119 oxidative phosphorylation
GO:0006754 ATP biosynthetic process
GO:1901843 positive regulation of high voltage-gated calcium channel activity
GO:2000984 negative regulation of ATP citrate synthase activity

Cellular Component:
GO:0005737 cytoplasm
GO:0005739 mitochondrion
GO:0005741 mitochondrial outer membrane
GO:0005887 integral component of plasma membrane
GO:0016020 membrane


-  Descriptions from all associated GenBank mRNAs
  AK315648 - Homo sapiens cDNA, FLJ96737.
AK097049 - Homo sapiens cDNA FLJ39730 fis, clone SMINT2015518, highly similar to Homo sapiens GBAS (GBAS) mRNA.
BC030821 - Homo sapiens glioblastoma amplified sequence, mRNA (cDNA clone MGC:23931 IMAGE:4808962), complete cds.
AF029786 - Homo sapiens GBAS (GBAS) mRNA, complete cds.
BC000732 - Homo sapiens glioblastoma amplified sequence, mRNA (cDNA clone MGC:1951 IMAGE:2959662), complete cds.
BC001837 - Homo sapiens glioblastoma amplified sequence, mRNA (cDNA clone MGC:4443 IMAGE:2959662), complete cds.
AJ001259 - Homo sapiens mRNA for NIPSNAP2 protein.
CU674374 - Synthetic construct Homo sapiens gateway clone IMAGE:100018736 5' read GBAS mRNA.
AB528140 - Synthetic construct DNA, clone: pF1KE0184, Homo sapiens GBAS gene for glioblastoma amplified sequence, without stop codon, in Flexi system.
AM392838 - Synthetic construct Homo sapiens clone IMAGE:100002319 for hypothetical protein (GBAS gene).
CR407612 - Homo sapiens full open reading frame cDNA clone RZPDo834A112D for gene GBAS, glioblastoma amplified sequence complete cds, without stopcodon.
DQ895508 - Synthetic construct Homo sapiens clone IMAGE:100009968; FLH185089.01L; RZPDo839F02145D glioblastoma amplified sequence (GBAS) gene, encodes complete protein.
BT007112 - Homo sapiens glioblastoma amplified sequence mRNA, complete cds.
DQ892309 - Synthetic construct clone IMAGE:100004939; FLH185093.01X; RZPDo839F02146D glioblastoma amplified sequence (GBAS) gene, encodes complete protein.
KJ891224 - Synthetic construct Homo sapiens clone ccsbBroadEn_00618 GBAS gene, encodes complete protein.
AK125036 - Homo sapiens cDNA FLJ43046 fis, clone BRTHA3003704, highly similar to Homo sapiens mRNA for NIPSNAP2 protein.
JD026896 - Sequence 7920 from Patent EP1572962.
JD032052 - Sequence 13076 from Patent EP1572962.
JD548890 - Sequence 529914 from Patent EP1572962.
JD368396 - Sequence 349420 from Patent EP1572962.
JD164639 - Sequence 145663 from Patent EP1572962.
JD289728 - Sequence 270752 from Patent EP1572962.
JD321530 - Sequence 302554 from Patent EP1572962.
JD454329 - Sequence 435353 from Patent EP1572962.
JD495132 - Sequence 476156 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: C9IYJ3, ENST00000322090.1, ENST00000322090.2, ENST00000322090.3, ENST00000322090.4, ENST00000322090.5, ENST00000322090.6, ENST00000322090.7, GBAS, NIPS2_HUMAN, NIPSNAP2 , NM_001483, O43801, O75323, Q53X96, uc317rey.1, uc317rey.2
UCSC ID: ENST00000322090.8_4
RefSeq Accession: NM_001483.3
Protein: O75323 (aka NIPS2_HUMAN or NPS2_HUMAN)

-  Gene Model Information
  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.