Human Gene SCAMP5 (uc002azk.2)
  Description: Homo sapiens secretory carrier membrane protein 5 (SCAMP5), transcript variant 3, mRNA.
Transcript (Including UTRs)
   Position: hg19 chr15:75,287,876-75,313,836 Size: 25,961 Total Exon Count: 7 Strand: +
Coding Region
   Position: hg19 chr15:75,304,181-75,311,324 Size: 7,144 Coding Exon Count: 6 

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

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr15:75,287,876-75,313,836)mRNA (may differ from genome)Protein (235 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
GeneNetworkH-INVHGNCHPRDLynxMGI
neXtProtOMIMPubMedUniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: SCAM5_HUMAN
DESCRIPTION: RecName: Full=Secretory carrier-associated membrane protein 5; Short=Secretory carrier membrane protein 5; Short=hSCAMP5;
FUNCTION: Required for the calcium-dependent exocytosis of signal sequence-containing cytokines such as CCL5. Probably acts in cooperation with the SNARE machinery. May play a role in accumulation of expanded polyglutamine (polyQ) protein huntingtin (HTT) in case of endoplasmic reticulum stress by inhibiting the endocytosis pathway.
SUBUNIT: Interacts (via C-terminal part) with SYT1 and SYT2; interaction with synaptotagmins making a link with the SNARE molecules. Interacts with SLC9A7.
INTERACTION: P46096:Syt1 (xeno); NbExp=2; IntAct=EBI-2695784, EBI-445340; P46097:Syt2 (xeno); NbExp=2; IntAct=EBI-2695784, EBI-457969;
SUBCELLULAR LOCATION: Cell membrane; Multi-pass membrane protein. Golgi apparatus membrane; Multi-pass membrane protein. Golgi apparatus, trans-Golgi network membrane; Multi-pass membrane protein. Recycling endosome membrane; Multi-pass membrane protein. Cytoplasmic vesicle, secretory vesicle, synaptic vesicle membrane; Multi-pass membrane protein (By similarity). Note=Mainly localizes in Golgi apparatus membrane. Upon calcium-triggered exocytosis, it translocates to the cell membrane. Highly enriched in synaptic vesicles (By similarity).
TISSUE SPECIFICITY: Expressed both by neuronal and non-neuronal tissues. Expressed in brain, stomach, thyroid, spinal cord, lymph node, trachea, adrenal gland, bone marrow and in the different parts of brain. In thyroid tissues, it is expressed by the follicular epithelial cells. In the adrenal gland tissues it is detected in the zona fasciculata of the cortex region (at protein level).
INDUCTION: By endoplasmic reticulum stress.
SIMILARITY: Belongs to the SCAMP family. SCAMP5 subfamily.

-  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

+  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: 122.59 RPKM in Brain - Frontal Cortex (BA9)
Total median expression: 1071.75 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 -105.70187-0.565 Picture PostScript Text
3' UTR -1088.592512-0.433 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
IPR007273 - SCAMP

Pfam Domains:
PF04144 - SCAMP family

ModBase Predicted Comparative 3D Structure on Q8TAC9
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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
Gene Details     
Gene Sorter     
  Ensembl   
  Protein Sequence   
  Alignment   

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

Biological Process:
GO:0006887 exocytosis
GO:0015031 protein transport
GO:0034976 response to endoplasmic reticulum stress
GO:0045806 negative regulation of endocytosis
GO:0045956 positive regulation of calcium ion-dependent exocytosis
GO:0050715 positive regulation of cytokine secretion

Cellular Component:
GO:0000139 Golgi membrane
GO:0005768 endosome
GO:0005794 Golgi apparatus
GO:0005886 plasma membrane
GO:0016020 membrane
GO:0016021 integral component of membrane
GO:0030054 cell junction
GO:0030672 synaptic vesicle membrane
GO:0031410 cytoplasmic vesicle
GO:0032588 trans-Golgi network membrane
GO:0045202 synapse
GO:0055038 recycling endosome membrane
GO:0031201 SNARE complex


-  Descriptions from all associated GenBank mRNAs
  AK126940 - Homo sapiens cDNA FLJ44993 fis, clone BRAWH3010461, highly similar to Secretory carrier-associated membrane protein 5.
AK056438 - Homo sapiens cDNA FLJ31876 fis, clone NT2RP7002478, highly similar to Secretory carrier-associated membrane protein 5.
AL834226 - Homo sapiens mRNA; cDNA DKFZp761D1321 (from clone DKFZp761D1321).
AB105192 - Homo sapiens SCAMP5 mRNA for secretory carrier membrane protein 5, complete cds.
AK301505 - Homo sapiens cDNA FLJ50896 complete cds, highly similar to Secretory carrier-associated membrane protein 5.
AF495715 - Homo sapiens secretory carrier membrane protein 5 mRNA, complete cds.
AK127480 - Homo sapiens cDNA FLJ45572 fis, clone BRTHA3010717, highly similar to Secretory carrier-associated membrane protein 5.
CR936761 - Homo sapiens mRNA; cDNA DKFZp686L1799 (from clone DKFZp686L1799).
BC024700 - Homo sapiens secretory carrier membrane protein 5, mRNA (cDNA clone MGC:24969 IMAGE:4941050), complete cds.
AB528299 - Synthetic construct DNA, clone: pF1KE0155, Homo sapiens SCAMP5 gene for secretory carrier membrane protein 5, without stop codon, in Flexi system.
AM393417 - Synthetic construct Homo sapiens clone IMAGE:100001764 for hypothetical protein (SCAMP5 gene).
CU692926 - Synthetic construct Homo sapiens gateway clone IMAGE:100016840 5' read SCAMP5 mRNA.
KJ895773 - Synthetic construct Homo sapiens clone ccsbBroadEn_05167 SCAMP5 gene, encodes complete protein.
AL833230 - Homo sapiens mRNA; cDNA DKFZp667P057 (from clone DKFZp667P057).
JD183071 - Sequence 164095 from Patent EP1572962.
JD566329 - Sequence 547353 from Patent EP1572962.
JD488860 - Sequence 469884 from Patent EP1572962.
JD380671 - Sequence 361695 from Patent EP1572962.
JD220967 - Sequence 201991 from Patent EP1572962.
JD054409 - Sequence 35433 from Patent EP1572962.
JD486619 - Sequence 467643 from Patent EP1572962.
JD230989 - Sequence 212013 from Patent EP1572962.
AK025678 - Homo sapiens cDNA: FLJ22025 fis, clone HEP08518.
JD502394 - Sequence 483418 from Patent EP1572962.
JD190911 - Sequence 171935 from Patent EP1572962.
JD121794 - Sequence 102818 from Patent EP1572962.
JD148948 - Sequence 129972 from Patent EP1572962.
JD401054 - Sequence 382078 from Patent EP1572962.
JD057900 - Sequence 38924 from Patent EP1572962.
JD455568 - Sequence 436592 from Patent EP1572962.
JD384303 - Sequence 365327 from Patent EP1572962.
JD384304 - Sequence 365328 from Patent EP1572962.
JD220553 - Sequence 201577 from Patent EP1572962.
AL360203 - Homo sapiens mRNA full length insert cDNA clone EUROIMAGE 222616.
JD151831 - Sequence 132855 from Patent EP1572962.
JD521424 - Sequence 502448 from Patent EP1572962.
JD555133 - Sequence 536157 from Patent EP1572962.
JD394212 - Sequence 375236 from Patent EP1572962.
JD244202 - Sequence 225226 from Patent EP1572962.
JD528794 - Sequence 509818 from Patent EP1572962.
JD261231 - Sequence 242255 from Patent EP1572962.
JD134481 - Sequence 115505 from Patent EP1572962.
JD268122 - Sequence 249146 from Patent EP1572962.
JD335154 - Sequence 316178 from Patent EP1572962.
JD099916 - Sequence 80940 from Patent EP1572962.
JD181602 - Sequence 162626 from Patent EP1572962.
JD478456 - Sequence 459480 from Patent EP1572962.
JD478457 - Sequence 459481 from Patent EP1572962.
JD195423 - Sequence 176447 from Patent EP1572962.
JD103967 - Sequence 84991 from Patent EP1572962.
JD115651 - Sequence 96675 from Patent EP1572962.
JD402348 - Sequence 383372 from Patent EP1572962.
JD555062 - Sequence 536086 from Patent EP1572962.
JD134228 - Sequence 115252 from Patent EP1572962.
JD532906 - Sequence 513930 from Patent EP1572962.
JD546675 - Sequence 527699 from Patent EP1572962.
JD176940 - Sequence 157964 from Patent EP1572962.
JD527230 - Sequence 508254 from Patent EP1572962.
JD438295 - Sequence 419319 from Patent EP1572962.
JD108776 - Sequence 89800 from Patent EP1572962.
JD214695 - Sequence 195719 from Patent EP1572962.
JD368722 - Sequence 349746 from Patent EP1572962.
JD178063 - Sequence 159087 from Patent EP1572962.
JD204523 - Sequence 185547 from Patent EP1572962.
JD062644 - Sequence 43668 from Patent EP1572962.
JD078065 - Sequence 59089 from Patent EP1572962.
JD299051 - Sequence 280075 from Patent EP1572962.
JD403462 - Sequence 384486 from Patent EP1572962.
JD528085 - Sequence 509109 from Patent EP1572962.
JD548981 - Sequence 530005 from Patent EP1572962.
JD426888 - Sequence 407912 from Patent EP1572962.
JD065908 - Sequence 46932 from Patent EP1572962.
JD120438 - Sequence 101462 from Patent EP1572962.
JD212025 - Sequence 193049 from Patent EP1572962.
JD504053 - Sequence 485077 from Patent EP1572962.
JD092266 - Sequence 73290 from Patent EP1572962.
JD120309 - Sequence 101333 from Patent EP1572962.
JD402848 - Sequence 383872 from Patent EP1572962.
JD165174 - Sequence 146198 from Patent EP1572962.
JD163816 - Sequence 144840 from Patent EP1572962.
JD166875 - Sequence 147899 from Patent EP1572962.
JD152818 - Sequence 133842 from Patent EP1572962.
JD560012 - Sequence 541036 from Patent EP1572962.
JD172828 - Sequence 153852 from Patent EP1572962.
JD465086 - Sequence 446110 from Patent EP1572962.
JD276804 - Sequence 257828 from Patent EP1572962.
JD288424 - Sequence 269448 from Patent EP1572962.
JD173082 - Sequence 154106 from Patent EP1572962.
JD123761 - Sequence 104785 from Patent EP1572962.
JD117772 - Sequence 98796 from Patent EP1572962.
JD232743 - Sequence 213767 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: B3KPJ7, B7Z762, D3DW71, NM_138967, NP_620417, Q8N3M4, Q8TAC9, SCAM5_HUMAN
UCSC ID: uc002azk.2
RefSeq Accession: NM_138967
Protein: Q8TAC9 (aka SCAM5_HUMAN or SCA5_HUMAN)
CCDS: CCDS45306.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_138967.3
exon count: 7CDS single in 3' UTR: no RNA size: 3433
ORF size: 708CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 1616.00frame shift in genome: no % Coverage: 99.24
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.