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SEC13 SEC13 homolog, nuclear pore and COPII coat complex component [ Homo sapiens (human) ]

Gene ID: 6396, updated on 7-Jun-2020

Summary

Official Symbol
SEC13provided by HGNC
Official Full Name
SEC13 homolog, nuclear pore and COPII coat complex componentprovided by HGNC
Primary source
HGNC:HGNC:10697
See related
Ensembl:ENSG00000157020 MIM:600152
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
SEC13R; npp-20; SEC13L1; D3S1231E
Summary
The protein encoded by this gene belongs to the SEC13 family of WD-repeat proteins. It is a constituent of the endoplasmic reticulum and the nuclear pore complex. It has similarity to the yeast SEC13 protein, which is required for vesicle biogenesis from endoplasmic reticulum during the transport of proteins. Multiple alternatively spliced transcript variants have been found. [provided by RefSeq, Oct 2008]
Expression
Ubiquitous expression in duodenum (RPKM 31.7), small intestine (RPKM 28.0) and 25 other tissues See more
Orthologs

Genomic context

See SEC13 in Genome Data Viewer
Location:
3p25.3
Exon count:
12
Annotation release Status Assembly Chr Location
109.20200522 current GRCh38.p13 (GCF_000001405.39) 3 NC_000003.12 (10300929..10321188, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (10342613..10362872, complement)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene TatD DNase domain containing 2 Neighboring gene long intergenic non-protein coding RNA 852 Neighboring gene microRNA 12127 Neighboring gene ghrelin opposite strand/antisense RNA Neighboring gene ghrelin and obestatin prepropeptide Neighboring gene ATPase plasma membrane Ca2+ transporting 2 Neighboring gene microRNA 378b Neighboring gene microRNA 885

Genomic regions, transcripts, and products

Expression

  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

HIV-1 interactions

Protein interactions

Protein Gene Interaction Pubs
Envelope surface glycoprotein gp120 env HIV-1 gp120/MBL complex co-localizes with intracellular COPII vesicle markers Sec31A and Sec13 in neuronal cells PubMed

Go to the HIV-1, Human Interaction Database

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
identical protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
structural molecule activity IEA
Inferred from Electronic Annotation
more info
 
Process Evidence Code Pubs
COPII vesicle coating TAS
Traceable Author Statement
more info
 
COPII-coated vesicle budding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
antigen processing and presentation of exogenous peptide antigen via MHC class II TAS
Traceable Author Statement
more info
 
antigen processing and presentation of peptide antigen via MHC class I TAS
Traceable Author Statement
more info
 
cargo loading into COPII-coated vesicle IDA
Inferred from Direct Assay
more info
PubMed 
intracellular protein transport NAS
Non-traceable Author Statement
more info
PubMed 
intracellular transport of virus TAS
Traceable Author Statement
more info
 
mRNA export from nucleus TAS
Traceable Author Statement
more info
 
positive regulation of TOR signaling IMP
Inferred from Mutant Phenotype
more info
PubMed 
positive regulation of TORC1 signaling IEA
Inferred from Electronic Annotation
more info
 
protein exit from endoplasmic reticulum IEA
Inferred from Electronic Annotation
more info
 
regulation of cellular response to heat TAS
Traceable Author Statement
more info
 
regulation of gene silencing by miRNA TAS
Traceable Author Statement
more info
 
regulation of glycolytic process TAS
Traceable Author Statement
more info
 
tRNA export from nucleus TAS
Traceable Author Statement
more info
 
viral process TAS
Traceable Author Statement
more info
 
viral transcription TAS
Traceable Author Statement
more info
 
Component Evidence Code Pubs
COPII vesicle coat IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
COPII vesicle coat IDA
Inferred from Direct Assay
more info
PubMed 
ER to Golgi transport vesicle membrane TAS
Traceable Author Statement
more info
 
GATOR2 complex IDA
Inferred from Direct Assay
more info
PubMed 
Golgi membrane IEA
Inferred from Electronic Annotation
more info
 
cytosol IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
cytosol TAS
Traceable Author Statement
more info
 
endoplasmic reticulum membrane TAS
Traceable Author Statement
more info
 
extracellular exosome HDA PubMed 
host cell IEA
Inferred from Electronic Annotation
more info
 
intracellular membrane-bounded organelle IDA
Inferred from Direct Assay
more info
 
colocalizes_with kinetochore IDA
Inferred from Direct Assay
more info
PubMed 
lysosomal membrane IDA
Inferred from Direct Assay
more info
PubMed 
nuclear envelope IDA
Inferred from Direct Assay
more info
PubMed 
nuclear pore outer ring IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
nuclear pore outer ring IDA
Inferred from Direct Assay
more info
PubMed 
nuclear pore outer ring NAS
Non-traceable Author Statement
more info
PubMed 
nucleoplasm IDA
Inferred from Direct Assay
more info
 

General protein information

Preferred Names
protein SEC13 homolog
Names
GATOR complex protein SEC13
SEC13 homolog, nuclear pore and COPII coating complex component
SEC13-like 1 isoform
SEC13-like protein 1
SEC13-related protein

NCBI Reference Sequences (RefSeq)

RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

  1. NM_001136026.3NP_001129498.1  protein SEC13 homolog isoform 3

    See identical proteins and their annotated locations for NP_001129498.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) represents the longest transcript and encodes the longest isoform (3).
    Source sequence(s)
    AK301999, BC091506
    Consensus CDS
    CCDS63540.1
    UniProtKB/Swiss-Prot
    P55735
    Related
    ENSP00000373312.2, ENST00000383801.6
    Conserved Domains (2) summary
    sd00039
    Location:107147
    7WD40; WD40 repeat [structural motif]
    cl25539
    Location:56335
    WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...
  2. NM_001136232.2NP_001129704.1  protein SEC13 homolog isoform 2

    See identical proteins and their annotated locations for NP_001129704.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR and the 5' coding region, and initiates translation at a downstream start codon compared to variant 3. It encodes isoform 2 which has a shorter N-terminus, compared to isoform 3.
    Source sequence(s)
    AF052155, BC002634, DB564012
    Consensus CDS
    CCDS46751.1
    UniProtKB/Swiss-Prot
    P55735
    Related
    ENSP00000380298.3, ENST00000397109.7
    Conserved Domains (2) summary
    sd00039
    Location:4787
    7WD40; WD40 repeat [structural motif]
    cl25539
    Location:11275
    WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...
  3. NM_001278946.1NP_001265875.1  protein SEC13 homolog isoform 5

    See identical proteins and their annotated locations for NP_001265875.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (5) differs in both UTRs and the 5' and 3' coding regions, compared to variant 3. It encodes isoform 5 which is shorter and has distinct N- and C-termini, compared to isoform 3.
    Source sequence(s)
    AA682381, AC022384, AK294662, CN344033
    UniProtKB/TrEMBL
    A8MWR8
    Related
    ENST00000397105.7
    Conserved Domains (3) summary
    COG2319
    Location:24155
    WD40; WD40 repeat [General function prediction only]
    sd00039
    Location:61101
    7WD40; WD40 repeat [structural motif]
    cl02567
    Location:25129
    WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...
  4. NM_030673.4NP_109598.2  protein SEC13 homolog isoform 4

    See identical proteins and their annotated locations for NP_109598.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) uses an alternate splice site in the 5' coding region and initiates translation at a downstream start codon, compared to variant 3. It encodes isoform 4, which is shorter at the N-terminus compared to isoform 3.
    Source sequence(s)
    BC002634, BC091506, CN344033
    UniProtKB/Swiss-Prot
    P55735
    Related
    ENSP00000336566.4, ENST00000337354.8
    Conserved Domains (3) summary
    COG2319
    Location:9304
    WD40; WD40 repeat [General function prediction only]
    sd00039
    Location:64104
    7WD40; WD40 repeat [structural motif]
    cl02567
    Location:13292
    WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...
  5. NM_183352.3NP_899195.1  protein SEC13 homolog isoform 1

    See identical proteins and their annotated locations for NP_899195.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) differs in the 5' UTR and lacks an exon in the 5' coding region, compared to variant 3. It encodes isoform 1 which has a shorter and distinct N-terminus, compared to isoform 3.
    Source sequence(s)
    BC091506, CN344033
    Consensus CDS
    CCDS2599.1
    UniProtKB/Swiss-Prot
    P55735
    Related
    ENSP00000312122.4, ENST00000350697.8
    Conserved Domains (2) summary
    sd00039
    Location:61101
    7WD40; WD40 repeat [structural motif]
    cl25539
    Location:10289
    WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000003.12 Reference GRCh38.p13 Primary Assembly

    Range
    10300929..10321188 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017007021.2XP_016862510.1  protein SEC13 homolog isoform X6

  2. XM_024453705.1XP_024309473.1  protein SEC13 homolog isoform X7

    Related
    ENSP00000380306.1, ENST00000397117.5
    Conserved Domains (2) summary
    sd00039
    Location:4787
    7WD40; WD40 repeat [structural motif]
    cl25539
    Location:11271
    WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...
  3. XM_024453704.1XP_024309472.1  protein SEC13 homolog isoform X5

    Conserved Domains (2) summary
    sd00039
    Location:4787
    7WD40; WD40 repeat [structural motif]
    cl25539
    Location:11275
    WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...
  4. XM_017007020.2XP_016862509.2  protein SEC13 homolog isoform X4

    Conserved Domains (2) summary
    sd00039
    Location:79119
    7WD40; WD40 repeat [structural motif]
    cl25539
    Location:28303
    WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...
  5. XM_005265379.3XP_005265436.1  protein SEC13 homolog isoform X3

    See identical proteins and their annotated locations for XP_005265436.1

    UniProtKB/Swiss-Prot
    P55735
    Conserved Domains (3) summary
    COG2319
    Location:9304
    WD40; WD40 repeat [General function prediction only]
    sd00039
    Location:64104
    7WD40; WD40 repeat [structural motif]
    cl02567
    Location:13292
    WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...
  6. XM_024453701.1XP_024309469.1  protein SEC13 homolog isoform X2

    Conserved Domains (2) summary
    sd00039
    Location:79119
    7WD40; WD40 repeat [structural motif]
    cl25539
    Location:28307
    WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...
  7. XM_024453703.1XP_024309471.1  protein SEC13 homolog isoform X1

    Conserved Domains (2) summary
    sd00039
    Location:107147
    7WD40; WD40 repeat [structural motif]
    cl25539
    Location:56335
    WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...
  8. XM_024453702.1XP_024309470.1  protein SEC13 homolog isoform X2

    Conserved Domains (2) summary
    sd00039
    Location:79119
    7WD40; WD40 repeat [structural motif]
    cl25539
    Location:28307
    WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...
  9. XM_017007019.1XP_016862508.1  protein SEC13 homolog isoform X1

    UniProtKB/Swiss-Prot
    P55735
    Conserved Domains (2) summary
    sd00039
    Location:107147
    7WD40; WD40 repeat [structural motif]
    cl25539
    Location:56335
    WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...
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