Human Gene NIPSNAP3A (ENST00000374767.5) from GENCODE V44
  Description: Homo sapiens nipsnap homolog 3A (NIPSNAP3A), transcript variant 1, mRNA. (from RefSeq NM_015469)
RefSeq Summary (NM_015469): NIPSNAP3A belongs to a family of proteins with putative roles in vesicular transport (Buechler et al., 2004 [PubMed 15177564]).[supplied by OMIM, Mar 2008].
Gencode Transcript: ENST00000374767.5
Gencode Gene: ENSG00000136783.10
Transcript (Including UTRs)
   Position: hg38 chr9:104,747,683-104,760,120 Size: 12,438 Total Exon Count: 6 Strand: +
Coding Region
   Position: hg38 chr9:104,747,793-104,759,338 Size: 11,546 Coding Exon Count: 6 

Page IndexSequence and LinksUniProtKB CommentsPrimersCTDRNA-Seq Expression
Microarray ExpressionRNA StructureProtein StructureOther SpeciesGO AnnotationsmRNA Descriptions
Other NamesMethods
Data last updated at UCSC: 2023-08-18 00:09:47

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr9:104,747,683-104,760,120)mRNA (may differ from genome)Protein (247 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGencodeGeneCards
HGNCHPRDLynxMGIneXtProtOMIM
PubMedUniProtKBBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: NPS3A_HUMAN
DESCRIPTION: RecName: Full=Protein NipSnap homolog 3A; Short=NipSnap3A; AltName: Full=Protein NipSnap homolog 4; Short=NipSnap4; AltName: Full=Target for Salmonella secreted protein C; Short=TassC;
SUBUNIT: Interacts with the Salmonella typhimurium virulence protein spiC.
INTERACTION: Q9H3D4:TP63; NbExp=2; IntAct=EBI-716291, EBI-2337775;
SUBCELLULAR LOCATION: Cytoplasm, cytosol. Note=May be part of some vesicular structure distinct from lysosomal vesicles.
TISSUE SPECIFICITY: Ubiquitous. Highly expressed in liver, kidney and muscle. Expressed at intermediate level in brain, heart, colon, thymus, kidney, small intestine, placenta, lung, leukocytes and spleen.
SIMILARITY: Belongs to the NipSnap family.
SEQUENCE CAUTION: Sequence=AAF28977.1; Type=Erroneous initiation;

-  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


-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 17.39 RPKM in Adrenal Gland
Total median expression: 466.43 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 -35.40110-0.322 Picture PostScript Text
3' UTR -149.61782-0.191 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

ModBase Predicted Comparative 3D Structure on Q9UFN0
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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 orthologGenome BrowserNo orthologNo orthologNo ortholog
      
      
  Ensembl   
  Protein Sequence   
  Alignment   

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005515 protein binding

Cellular Component:
GO:0005634 nucleus
GO:0005737 cytoplasm
GO:0005739 mitochondrion
GO:0005829 cytosol


-  Descriptions from all associated GenBank mRNAs
  BC005935 - Homo sapiens nipsnap homolog 3A (C. elegans), mRNA (cDNA clone MGC:14553 IMAGE:4064889), complete cds.
AK301410 - Homo sapiens cDNA FLJ58863 complete cds, highly similar to Protein NipSnap3A.
AF161417 - Homo sapiens HSPC299 mRNA, partial cds.
AK024015 - Homo sapiens cDNA FLJ13953 fis, clone Y79AA1001078.
AL117557 - Homo sapiens mRNA; cDNA DKFZp564D177 (from clone DKFZp564D177).
BC045830 - Homo sapiens nipsnap homolog 3A (C. elegans), mRNA (cDNA clone IMAGE:5264683).
HQ448740 - Synthetic construct Homo sapiens clone IMAGE:100072186; CCSB005699_01 nipsnap homolog 3A (C. elegans) (NIPSNAP3A) gene, encodes complete protein.
KJ893494 - Synthetic construct Homo sapiens clone ccsbBroadEn_02888 NIPSNAP3A gene, encodes complete protein.
CU675195 - Synthetic construct Homo sapiens gateway clone IMAGE:100017622 5' read NIPSNAP3A mRNA.
JD021909 - Sequence 2933 from Patent EP1572962.
JD024063 - Sequence 5087 from Patent EP1572962.
JD027080 - Sequence 8104 from Patent EP1572962.
JD034147 - Sequence 15171 from Patent EP1572962.
JD031676 - Sequence 12700 from Patent EP1572962.
JD241680 - Sequence 222704 from Patent EP1572962.
JD170421 - Sequence 151445 from Patent EP1572962.
JD239209 - Sequence 220233 from Patent EP1572962.
JD350586 - Sequence 331610 from Patent EP1572962.
JD510059 - Sequence 491083 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: A6NM55, ENST00000374767.1, ENST00000374767.2, ENST00000374767.3, ENST00000374767.4, HSPC299, NIPSNAP4, NM_015469, NPS3A_HUMAN, Q5VX32, Q9BRV7, Q9H843, Q9P083, Q9UFN0, uc004bch.1, uc004bch.2
UCSC ID: ENST00000374767.5
RefSeq Accession: NM_015469
Protein: Q9UFN0 (aka NPS3A_HUMAN or NP3A_HUMAN)
CCDS: CCDS6760.1

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