Human Gene SEC22A (uc003ege.3) Description and Page Index
  Description: Homo sapiens SEC22 vesicle trafficking protein homolog A (S. cerevisiae) (SEC22A), mRNA.
RefSeq Summary (NM_012430): The protein encoded by this gene belongs to the member of the SEC22 family of vesicle trafficking proteins. This protein has similarity to rat SEC22 and may act in the early stages of the secretory pathway. [provided by RefSeq, Nov 2008]. ##Evidence-Data-START## Transcript exon combination :: SRR1660807.96762.1, SRR1803617.119793.1 [ECO:0000332] RNAseq introns :: single sample supports all introns SAMEA1965299, SAMEA1966682 [ECO:0000348] ##Evidence-Data-END## ##RefSeq-Attributes-START## MANE Ensembl match :: ENST00000492595.6/ ENSP00000417972.1 RefSeq Select criteria :: based on conservation, expression, longest protein ##RefSeq-Attributes-END##
Transcript (Including UTRs)
   Position: hg19 chr3:122,920,774-122,992,982 Size: 72,209 Total Exon Count: 7 Strand: +
Coding Region
   Position: hg19 chr3:122,928,065-122,990,569 Size: 62,505 Coding Exon Count: 6 

Page IndexSequence and LinksUniProtKB CommentsGenetic AssociationsCTDGene 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 (chr3:122,920,774-122,992,982)mRNA (may differ from genome)Protein (307 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaBioGPS
CGAPEnsemblEntrez GeneExonPrimerGeneCardsGeneNetwork
OMIMPubMedReactomeStanford SOURCETreefamUniProtKB

-  Comments and Description Text from UniProtKB
DESCRIPTION: RecName: Full=Vesicle-trafficking protein SEC22a; AltName: Full=SEC22 vesicle-trafficking protein homolog A; AltName: Full=SEC22 vesicle-trafficking protein-like 2;
FUNCTION: May be involved in vesicle transport between the ER and the Golgi complex (By similarity).
SUBCELLULAR LOCATION: Endoplasmic reticulum membrane; Multi-pass membrane protein (By similarity).
SIMILARITY: Belongs to the synaptobrevin family.
SIMILARITY: Contains 1 longin domain.
SEQUENCE CAUTION: Sequence=AAD43013.1; Type=Frameshift; Positions=265, 288;

-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): SEC22A
CDC HuGE Published Literature: SEC22A

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

+  Common Gene Haplotype Alleles
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-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 8.72 RPKM in Testis
Total median expression: 165.61 RPKM

View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
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-  mRNA Secondary Structure of 3' and 5' UTRs
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -25.6079-0.324 Picture PostScript Text
3' UTR -667.082413-0.276 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
IPR011012 - Longin-like_dom
IPR010908 - Longin_dom

Pfam Domains:
PF13774 - Regulated-SNARE-like domain

SCOP Domains:
64356 - SNARE-like

ModBase Predicted Comparative 3D Structure on Q96IW7
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 BrowserNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
Gene SorterGene Sorter    
 Protein Sequence    

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0000149 SNARE binding
GO:0005215 transporter activity
GO:0005484 SNAP receptor activity
GO:0005515 protein binding

Biological Process:
GO:0006888 ER to Golgi vesicle-mediated transport
GO:0015031 protein transport
GO:0016192 vesicle-mediated transport
GO:0048280 vesicle fusion with Golgi apparatus
GO:0006887 exocytosis

Cellular Component:
GO:0005783 endoplasmic reticulum
GO:0005789 endoplasmic reticulum membrane
GO:0016020 membrane
GO:0016021 integral component of membrane
GO:0031201 SNARE complex

-  Descriptions from all associated GenBank mRNAs
  LF210600 - JP 2014500723-A/18103: Polycomb-Associated Non-Coding RNAs.
AK315771 - Homo sapiens cDNA, FLJ96885, Homo sapiens SEC22 vesicle trafficking protein-like 2 (S.cerevisiae) (SEC22L2), mRNA.
AF100749 - Homo sapiens Sec22 homolog mRNA, complete cds.
AK057587 - Homo sapiens cDNA FLJ33025 fis, clone THYMU1000558, highly similar to Homo sapiens SEC22 vesicle trafficking protein-like 2 (S. cerevisiae) (SEC22L2), mRNA.
BC007122 - Homo sapiens SEC22 vesicle trafficking protein homolog A (S. cerevisiae), mRNA (cDNA clone MGC:4981 IMAGE:3459649), complete cds.
CU675551 - Synthetic construct Homo sapiens gateway clone IMAGE:100018808 5' read SEC22A mRNA.
HQ447819 - Synthetic construct Homo sapiens clone IMAGE:100071162; CCSB002725_02 SEC22 vesicle trafficking protein homolog A (S. cerevisiae) (SEC22A) gene, encodes complete protein.
KJ893583 - Synthetic construct Homo sapiens clone ccsbBroadEn_02977 SEC22A gene, encodes complete protein.
MA446177 - JP 2018138019-A/18103: Polycomb-Associated Non-Coding RNAs.
JD342756 - Sequence 323780 from Patent EP1572962.
JD281646 - Sequence 262670 from Patent EP1572962.
JD339485 - Sequence 320509 from Patent EP1572962.
JD204501 - Sequence 185525 from Patent EP1572962.
JD482514 - Sequence 463538 from Patent EP1572962.
JD302670 - Sequence 283694 from Patent EP1572962.
JD106749 - Sequence 87773 from Patent EP1572962.
JD471134 - Sequence 452158 from Patent EP1572962.
JD324328 - Sequence 305352 from Patent EP1572962.
JD370218 - Sequence 351242 from Patent EP1572962.
JD370217 - Sequence 351241 from Patent EP1572962.
JD167661 - Sequence 148685 from Patent EP1572962.
JD481345 - Sequence 462369 from Patent EP1572962.

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

Protein Q96IW7 (Reactome details) participates in the following event(s):

R-HSA-204008 SEC31:SEC13 and v-SNARE recruitment
R-HSA-5694425 NSF ATPase activity dissociates cis-SNARE
R-HSA-203973 Vesicle budding
R-HSA-5694446 BET1:GOSR2:STX5 bind v-SNARES on tethered vesicle
R-HSA-5694441 CSNK1D phosphorylates SEC23
R-HSA-5694439 COPII coat binds TRAPPCII and RAB1:GDP
R-HSA-5694423 NSF and SNAPs bind cis-SNARE complex
R-HSA-5694418 RAB1:GTP binds USO1 and GORASP1:GOLGA2
R-HSA-5694409 Nucleotide exchange on RAB1
R-HSA-204005 COPII-mediated vesicle transport
R-HSA-199977 ER to Golgi Anterograde Transport
R-HSA-199991 Membrane Trafficking
R-HSA-948021 Transport to the Golgi and subsequent modification
R-HSA-5653656 Vesicle-mediated transport
R-HSA-446203 Asparagine N-linked glycosylation
R-HSA-597592 Post-translational protein modification
R-HSA-392499 Metabolism of proteins

-  Other Names for This Gene
  Alternate Gene Symbols: B2RE26, NM_012430, NP_036562, Q96IW7, Q9Y682, SC22A_HUMAN, SEC22L2
UCSC ID: uc003ege.3
RefSeq Accession: NM_012430
Protein: Q96IW7 (aka SC22A_HUMAN)
CCDS: CCDS3021.1

-  Gene Model Information
category: coding nonsense-mediated-decay: no RNA accession: NM_012430.4
exon count: 7CDS single in 3' UTR: no RNA size: 3429
ORF size: 924CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 1982.00frame shift in genome: no % Coverage: 99.62
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
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-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.