sec13 (SPBC215.15)


Gene Standard Namesec13 Characterisation Statuspublished
Systematic IDSPBC215.15 Feature Typeprotein coding
Synonyms Name Description
ProductCOPII-coated vesicle component Sec13 Product Size297aa, 32.57 kDa
Genomic Location Chromosome II, 4059950-4061230 (1281nt); CDS:4060033-4061002 (970nt)

Ensembl Gene Location
GO Biological Process
Term NameCount
ER to Golgi vesicle-mediated transport74
Annotation ExtensionEvidenceWith/FromReference
intracellular protein transport342
Annotation ExtensionEvidenceWith/FromReference
nuclear pore organization2
Annotation ExtensionEvidenceWith/FromReference
GO Cellular Component
Term NameCount
COPII vesicle coat9
Annotation ExtensionEvidenceWith/FromReference
cytoplasm4209
Annotation ExtensionEvidenceWith/FromReference
cytosol2314
Annotation ExtensionEvidenceWith/FromReference
endoplasmic reticulum596
Annotation ExtensionEvidenceWith/FromReference
nuclear pore52
Annotation ExtensionEvidenceWith/FromReference
nucleus2696
Annotation ExtensionEvidenceWith/FromReference
plasma membrane249
Annotation ExtensionEvidenceWith/FromReference
Seh1-associated complex8
Annotation ExtensionEvidenceWith/FromReference
Target Of
OntologyRelationshipGeneProduct
FYPO affected by mutation in hub1 ubiquitin-like protein modifier Hub1
FYPO affected by mutation in snu66 U4/U6 x U5 tri-snRNP complex subunit Snu66
Transcript
Ensembl transcript structure with UTRs, exons and introns

Transcript Structure

Region Coordinates Reference
Exons4059950..4060068, 4060145..4061230
mRNA4059950..4061230
5' UTR4059950..4060032PMID:21511999
CDS4060033..4060068, 4060145..4061002
3' UTR4061003..4061230PMID:21511999
Protein Features

Graphical View

Ensembl protein image with mapped locations of structural domains

Protein Families and Domains

Feature ID Database InterPro Description Start End Count
PF00400 Pfam IPR001680 WD40 repeat 200 236 104
PF00400 Pfam IPR001680 WD40 repeat 138 186 104
PF00400 Pfam IPR001680 WD40 repeat 14 37 104
PF00400 Pfam IPR001680 WD40 repeat 93 127 104
PF00400 Pfam IPR001680 WD40 repeat 45 82 104
SM00320 SMART IPR001680 WD40 repeat 245 283 112
SM00320 SMART IPR001680 WD40 repeat 194 237 112
SM00320 SMART IPR001680 WD40 repeat 134 187 112
SM00320 SMART IPR001680 WD40 repeat 1 37 112
SM00320 SMART IPR001680 WD40 repeat 88 129 112
SM00320 SMART IPR001680 WD40 repeat 42 83 112
PS50294 Prosite Profiles IPR017986 WD40-repeat-containing domain 5 246 104
PS50082 Prosite Profiles IPR001680 WD40 repeat 201 236 100
PS50082 Prosite Profiles IPR001680 WD40 repeat 49 82 100
PTHR11024 HMMPANTHER 1 297 2
2.130.10.10 Gene3D IPR015943 WD40/YVTN repeat-like-containing domain 6 294 145
SSF50978 SuperFamily IPR017986 WD40-repeat-containing domain 10 289 135

View domain organization at Pfam

Manually Curated Family or Sub-families

Term IDTerm NameReferenceCount
PBO:0000190WD repeat proteinTemporary processing gif - replaced by AJAX with count of genes annotated with the term PBO:0000190

Protein Properties

Ave. residue weight 109.66 Da
Charge -7.00
Isoelectric point 5.11
Molecular weight 32.57 kDa
Number of residues 297
Sequence
Gene Expression

Quantitative Gene Expression

Protein Level

Molecules/Cell (average)ExtensionConditionScaleEvidenceReference
55757during GO:0000080PECO:0000126,
PECO:0000005
single cellmass spectrometry evidencePMID:24763107
55570during GO:0000084PECO:0000126,
PECO:0000005
single cellmass spectrometry evidencePMID:24763107
57145during GO:0000085PECO:0000126,
PECO:0000005
single cellmass spectrometry evidencePMID:24763107
51393during GO:0000087PECO:0000126,
PECO:0000005
single cellmass spectrometry evidencePMID:24763107
54497during GO:0072690PECO:0000126,
PECO:0000005
single cellmass spectrometry evidencePMID:24763107
49137.4during GO:0072690PECO:0000005,
PECO:0000014
population wideexperimental evidencePMID:23101633
32755.82during cell quiescence following G1 arrest due to nitrogen limitationPECO:0000005,
PECO:0000014,
PECO:0000127
population wideexperimental evidencePMID:23101633

RNA Level

Molecules/Cell (average)ExtensionConditionScaleEvidenceReference
8.4during GO:0072690PECO:0000005,
PECO:0000014
population wideexperimental evidencePMID:23101633
1.2during cell quiescence following G1 arrest due to nitrogen limitationPECO:0000005,
PECO:0000014,
PECO:0000127
population wideexperimental evidencePMID:23101633
Species Distribution
DescriptionQualifierReferenceCount
predominantly single copy (one to one)3092
conserved in fungi4603
conserved in eukaryotes4514
conserved in metazoa3424
conserved in vertebrates3399
conserved in eukaryotes only2501
Orthologs

Manually curated orthologous groups

SpeciesGeneDescriptionLinksCount

Orthologs in Compara


Physical Interactions

Source: BioGRID

View all interactions in esyN
View the HCPIN interactions in esyN

Gene Product Evidence Reference
forms complex withnup189nucleoporin Nup98 and Nup96 Reconstituted ComplexPMID:22955883
binds activation domain construct withsec31COPII-coated vesicle component Sec31 (predicted) Two-hybridPMID:23695164
External References
Database Identifier Description
NBRP SPBC215.15 Fission yeast strain database, National BioResource Project (Japan)
YOGY SPBC215.15 Retrieval of eukaryotic orthologs (Bähler Lab)
BioGrid SPBC215.15 BioGRID Interaction Datasets
Expression Viewer SPBC215.15 Cell Cycle Expression Profile (Bähler Lab)
Expression Viewer SPBC215.15 Meiosis/Sporulation Expression Profies (Bähler Lab)
Expression Viewer SPBC215.15 Pheromone response/mating expression profiles (Bähler Lab)
Expression Viewer SPBC215.15 Environmental stress expression profiles (Bähler Lab)
Pomb(A) SPBC215.15 Polyadenylation Viewer (Gullerova lab)
pombeTV SPBC215.15 Transcriptome Viewer (Bähler Lab)
GEO SPBC215.15 GEO profiles
PInt SPBC215.15 Protein-Protein Interaction Predictor (Bähler Lab)
PeptideAtlas SPBC215.15 Peptides identified in tandem mass spectrometry proteomics experiments
SYSGRO SPBC215.15 Fission yeast phenotypic data & analysis
Cyclebase SPBC215.15.1 Cell Cycle Data
SPD / RIKEN13/13G12Orfeome Localization Data
UniProtKB/SwissProtO94319Protein transport protein sec13
ModBaseO94319Database of comparative protein structure models
STRINGO94319Network display of known and predicted interactions and functional associations
RefSeq PeptideNP_596692COPII-coated vesicle component Sec13
RefSeq mRNANM_001022615972h- COPII-coated vesicle component Sec13 (sec13), mRNA
European Nucleotide ArchiveCAA22129.1ENA Protein Mapping
UniParcUPI000006AA3EUniProt Archive

Literature for sec13

Search: Europe PMC or PubMed

Release Version: PomBase:26_53 - 27 May 2015