Human Gene SNAPIN (uc001fcq.4) Description and Page Index
  Description: Homo sapiens SNAP-associated protein (SNAPIN), transcript variant 1, mRNA.
RefSeq Summary (NM_012437): The protein encoded by this gene is a coiled-coil-forming protein that associates with the SNARE (soluble N-ethylmaleimide-sensitive fusion protein attachment protein receptor) complex of proteins and the BLOC-1 (biogenesis of lysosome-related organelles) complex. Biochemical studies have identified additional binding partners. As part of the SNARE complex, it is required for vesicle docking and fusion and regulates neurotransmitter release. The BLOC-1 complex is required for the biogenesis of specialized organelles such as melanosomes and platelet dense granules. Mutations in gene products that form the BLOC-1 complex have been identified in mouse strains that are models of Hermansky-Pudlak syndrome. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jun 2012].
Transcript (Including UTRs)
   Position: hg19 chr1:153,631,130-153,634,328 Size: 3,199 Total Exon Count: 4 Strand: +
Coding Region
   Position: hg19 chr1:153,631,220-153,633,777 Size: 2,558 Coding Exon Count: 4 

Page IndexSequence and LinksUniProtKB CommentsMalaCardsCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr1:153,631,130-153,634,328)mRNA (may differ from genome)Protein (136 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
BioGPSCGAPEnsemblEntrez GeneExonPrimerGeneCards
GeneNetworkH-INVHGNCHPRDLynxMGI
neXtProtOMIMPubMedReactomeStanford SOURCEUniProtKB
Wikipedia

-  Comments and Description Text from UniProtKB
  ID: SNAPN_HUMAN
DESCRIPTION: RecName: Full=SNARE-associated protein Snapin; AltName: Full=Biogenesis of lysosome-related organelles complex 1 subunit 7; Short=BLOC-1 subunit 7; AltName: Full=Synaptosomal-associated protein 25-binding protein; Short=SNAP-associated protein;
FUNCTION: Component of the BLOC-1 complex, a complex that is required for normal biogenesis of lysosome-related organelles (LRO), such as platelet dense granules and melanosomes. In concert with the AP-3 complex, the BLOC-1 complex is required to target membrane protein cargos into vesicles assembled at cell bodies for delivery into neurites and nerve terminals. The BLOC-1 complex, in association with SNARE proteins, is also proposed to be involved in neurite extension. Plays a role in intracellular vesicle trafficking. May modulate a step between vesicle priming, fusion and calcium-dependent neurotransmitter release through its ability to potentiate the interaction of synaptotagmin with the SNAREs and the plasma-membrane-associated protein SNAP25. Its phosphorylation state influences exocytotic protein interactions and may regulate synaptic vesicle exocytosis. May also have a role in the mechanisms of SNARE-mediated membrane fusion in non-neuronal cells.
SUBUNIT: Interacts with CSNK1D, SNAP23 and STX4A but not with STX1A, VAMP2 and SYT1. Interacts with SNAP25; the interaction with SNAP25 is increased by its phosphorylation (By similarity). Component of the biogenesis of lysosome-related organelles complex 1 (BLOC-1) composed of BLOC1S1, BLOC1S2, BLOC1S3, BLOC1S4, BLOC1S5, BLOC1S6, DTNBP1/BLOC1S7 and SNAPIN/BLOC1S8. Octamer composed of one copy each BLOC1S1, BLOC1S2, BLOC1S3, BLOC1S4, BLOC1S5, BLOC1S6, DTNBP1/BLOC1S7 and SNAPIN/BLOC1S8. The BLOC-1 complex associates with the AP-3 protein complex and membrane protein cargos. Associates with the SNARE complex. Interacts with CEP110, NANOS1, PUM2 and RGS7. Interacts with human cytomegalovirus/HHV-5 protein UL70.
INTERACTION: Q6QNY1:BLOC1S2; NbExp=7; IntAct=EBI-296723, EBI-465872; Q96EV8:DTNBP1; NbExp=4; IntAct=EBI-296723, EBI-465804; O75923:DYSF; NbExp=3; IntAct=EBI-296723, EBI-2799016; Q9UL45:PLDN; NbExp=2; IntAct=EBI-296723, EBI-465781; Q15849-1:SLC14A2; NbExp=5; IntAct=EBI-296723, EBI-1633392; Q62668-1:Slc14a2 (xeno); NbExp=6; IntAct=EBI-296723, EBI-1635608; P11277:SPTB; NbExp=3; IntAct=EBI-296723, EBI-514908;
SUBCELLULAR LOCATION: Cytoplasm (By similarity). Membrane; Peripheral membrane protein; Cytoplasmic side (By similarity). Cytoplasmic vesicle membrane; Peripheral membrane protein; Cytoplasmic side (By similarity). Cytoplasmic vesicle, secretory vesicle, synaptic vesicle membrane; Peripheral membrane protein; Cytoplasmic side (Potential). Cell junction, synapse, synaptosome. Cytoplasm, perinuclear region. Golgi apparatus membrane (By similarity). Note=May be cytoplasmic and peripheral membrane bound or anchored to the vesicular membrane through an N-terminal signal anchor (By similarity). Co-localizes with NANOS1 and PUM2 in the perinuclear region of germ cells.
TISSUE SPECIFICITY: Expressed in male germ cells of adult testis (at protein level).
DEVELOPMENTAL STAGE: Expressed in germ cells of 22-week prenatal testis.
PTM: Phosphorylated by CSNK1D/CK1 (By similarity).
SIMILARITY: Belongs to the SNAPIN family.

-  MalaCards Disease Associations
  MalaCards Gene Search: SNAPIN
Diseases sorted by gene-association score: tricuspid valve stenosis (2)

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

+  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: 28.20 RPKM in Adrenal Gland
Total median expression: 882.19 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 -37.4090-0.416 Picture PostScript Text
3' UTR -156.23551-0.284 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
IPR017246 - Snapin

Pfam Domains:
PF14712 - Snapin/Pallidin

ModBase Predicted Comparative 3D Structure on O95295
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 orthologGenome BrowserGenome BrowserGenome BrowserGenome BrowserNo ortholog
Gene DetailsGene Details Gene DetailsGene Details 
Gene SorterGene Sorter Gene SorterGene Sorter 
 RGDEnsemblFlyBaseWormBase 
 Protein SequenceProtein SequenceProtein SequenceProtein Sequence 
 AlignmentAlignmentAlignmentAlignment 

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0000149 SNARE binding
GO:0005515 protein binding

Biological Process:
GO:0006886 intracellular protein transport
GO:0006887 exocytosis
GO:0007040 lysosome organization
GO:0007042 lysosomal lumen acidification
GO:0007268 chemical synaptic transmission
GO:0007269 neurotransmitter secretion
GO:0008089 anterograde axonal transport
GO:0008090 retrograde axonal transport
GO:0008333 endosome to lysosome transport
GO:0010977 negative regulation of neuron projection development
GO:0016032 viral process
GO:0016079 synaptic vesicle exocytosis
GO:0016188 synaptic vesicle maturation
GO:0031175 neuron projection development
GO:0031629 synaptic vesicle fusion to presynaptic active zone membrane
GO:0032418 lysosome localization
GO:0032438 melanosome organization
GO:0034629 cellular protein complex localization
GO:0043393 regulation of protein binding
GO:0048489 synaptic vesicle transport
GO:0048490 anterograde synaptic vesicle transport
GO:0051604 protein maturation
GO:0072553 terminal button organization
GO:0097352 autophagosome maturation
GO:1902774 late endosome to lysosome transport
GO:1902824 positive regulation of late endosome to lysosome transport

Cellular Component:
GO:0000139 Golgi membrane
GO:0005737 cytoplasm
GO:0005764 lysosome
GO:0005765 lysosomal membrane
GO:0005794 Golgi apparatus
GO:0005829 cytosol
GO:0008021 synaptic vesicle
GO:0016020 membrane
GO:0030054 cell junction
GO:0030141 secretory granule
GO:0030672 synaptic vesicle membrane
GO:0031083 BLOC-1 complex
GO:0031410 cytoplasmic vesicle
GO:0045202 synapse
GO:0048471 perinuclear region of cytoplasm
GO:0099078 BORC complex
GO:1904115 axon cytoplasm


-  Descriptions from all associated GenBank mRNAs
  AK024555 - Homo sapiens cDNA: FLJ20902 fis, clone ADSE00189.
LF206201 - JP 2014500723-A/13704: Polycomb-Associated Non-Coding RNAs.
BC004494 - Homo sapiens SNAP-associated protein, mRNA (cDNA clone MGC:11087 IMAGE:3830132), complete cds.
BC000761 - Homo sapiens SNAP-associated protein, mRNA (cDNA clone MGC:2717 IMAGE:2821705), complete cds.
AB590618 - Synthetic construct DNA, clone: pFN21AE1622, Homo sapiens SNAPIN gene for SNAP-associated protein, without stop codon, in Flexi system.
BT006753 - Homo sapiens SNARE associated protein snapin mRNA, complete cds.
KJ898509 - Synthetic construct Homo sapiens clone ccsbBroadEn_07903 SNAPIN gene, encodes complete protein.
AF086837 - Homo sapiens snapin mRNA, complete cds.
JD377803 - Sequence 358827 from Patent EP1572962.
JD236264 - Sequence 217288 from Patent EP1572962.
JD562372 - Sequence 543396 from Patent EP1572962.
JD543643 - Sequence 524667 from Patent EP1572962.
JD154155 - Sequence 135179 from Patent EP1572962.
JD566366 - Sequence 547390 from Patent EP1572962.
LF352382 - JP 2014500723-A/159885: Polycomb-Associated Non-Coding RNAs.
JD243774 - Sequence 224798 from Patent EP1572962.
JD495689 - Sequence 476713 from Patent EP1572962.
JD525038 - Sequence 506062 from Patent EP1572962.
JD565458 - Sequence 546482 from Patent EP1572962.
JD473038 - Sequence 454062 from Patent EP1572962.
JD264760 - Sequence 245784 from Patent EP1572962.
MA587959 - JP 2018138019-A/159885: Polycomb-Associated Non-Coding RNAs.
MA441778 - JP 2018138019-A/13704: Polycomb-Associated Non-Coding RNAs.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein O95295 (Reactome details) participates in the following event(s):

R-HSA-421836 trans-Golgi Network Derived Vesicle Uncoating
R-HSA-421833 Vamp And trans-Golgi Network AP-1 Binding Coupled With Cargo Capture
R-HSA-421835 trans-Golgi Network Vesicle Scission
R-HSA-421831 trans-Golgi Network Coat Assembly
R-HSA-432722 Golgi Associated Vesicle Biogenesis
R-HSA-421837 Clathrin derived vesicle budding
R-HSA-199992 trans-Golgi Network Vesicle Budding
R-HSA-199991 Membrane Trafficking
R-HSA-5653656 Vesicle-mediated transport

-  Other Names for This Gene
  Alternate Gene Symbols: BLOC1S7, D3DV56, NM_012437, NP_036569, O95295, Q5SXU8, SNAP25BP, SNAPAP, SNAPN_HUMAN, uc001fcq.3
UCSC ID: uc001fcq.4
RefSeq Accession: NM_012437
Protein: O95295 (aka SNAPN_HUMAN)
CCDS: CCDS1049.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_012437.5
exon count: 4CDS single in 3' UTR: no RNA size: 1052
ORF size: 411CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 1022.00frame shift in genome: no % Coverage: 100.00
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.