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

    Gene ID: 6396, updated on 10-Oct-2024

    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; AllianceGenome:HGNC:10697
    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
    NEW
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    Genomic context

    See SEC13 in Genome Data Viewer
    Location:
    3p25.3
    Exon count:
    12
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (10300931..10321112, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (10294231..10314421, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (10342615..10362796, complement)

    Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene TatD DNase domain containing 2 Neighboring gene Sharpr-MPRA regulatory region 7129 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:10329829-10330444 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:10332275-10332877 Neighboring gene Sharpr-MPRA regulatory region 4342 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19422 Neighboring gene long intergenic non-protein coding RNA 852 Neighboring gene microRNA 12127 Neighboring gene ghrelin opposite strand/antisense RNA Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:10362509-10363104 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:10369968-10370516 Neighboring gene ghrelin and obestatin prepropeptide Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:10380971-10381538 Neighboring gene ReSE screen-validated silencer GRCh37_chr3:10394060-10394233 Neighboring gene ATPase plasma membrane Ca2+ transporting 2 Neighboring gene microRNA 378b Neighboring gene MPRA-validated peak4536 silencer Neighboring gene microRNA 885

    Genomic regions, transcripts, and products

    Expression

    • Project title: HPA RNA-seq normal tissues 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

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables identical protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables structural molecule activity IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    Process Evidence Code Pubs
    involved_in COPII-coated vesicle budding IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in COPII-coated vesicle cargo loading IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in cellular response to nutrient levels IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in intracellular protein transport NAS
    Non-traceable Author Statement
    more info
    PubMed 
    involved_in mRNA transport IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in negative regulation of TORC1 signaling NAS
    Non-traceable Author Statement
    more info
    PubMed 
    involved_in nucleocytoplasmic transport NAS
    Non-traceable Author Statement
    more info
    PubMed 
    involved_in positive regulation of TOR signaling IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in positive regulation of TORC1 signaling IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in positive regulation of TORC1 signaling NAS
    Non-traceable Author Statement
    more info
    PubMed 
    involved_in protein exit from endoplasmic reticulum IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in protein import into nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    Component Evidence Code Pubs
    part_of COPII vesicle coat IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    part_of COPII vesicle coat IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in ER to Golgi transport vesicle membrane TAS
    Traceable Author Statement
    more info
     
    part_of GATOR2 complex IDA
    Inferred from Direct Assay
    more info
    PubMed 
    part_of GATOR2 complex NAS
    Non-traceable Author Statement
    more info
    PubMed 
    located_in cytosol TAS
    Traceable Author Statement
    more info
     
    located_in endoplasmic reticulum membrane TAS
    Traceable Author Statement
    more info
     
    located_in extracellular exosome HDA PubMed 
    located_in intracellular membrane-bounded organelle IDA
    Inferred from Direct Assay
    more info
     
    colocalizes_with kinetochore IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in lysosomal membrane IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in lysosomal membrane TAS
    Traceable Author Statement
    more info
     
    located_in nuclear envelope IDA
    Inferred from Direct Assay
    more info
    PubMed 
    part_of nuclear pore NAS
    Non-traceable Author Statement
    more info
    PubMed 
    part_of nuclear pore outer ring IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    part_of nuclear pore outer ring IDA
    Inferred from Direct Assay
    more info
    PubMed 
    part_of nuclear pore outer ring NAS
    Non-traceable Author Statement
    more info
    PubMed 
    located_in nucleoplasm IDA
    Inferred from Direct Assay
    more info
     

    General protein information

    Preferred Names
    protein SEC13 homolog
    Names
    GATOR complex protein SEC13
    GATOR2 complex protein SEC13
    SEC13 homolog, nuclear pore and COPII coating complex component
    SEC13-like protein 1
    SEC13-related protein

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    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/TrEMBL
      Q53GB2
      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_001136232.3NP_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
      Consensus CDS
      CCDS46751.1
      UniProtKB/TrEMBL
      Q53GB2
      Related
      ENSP00000380298.3, ENST00000397109.7
      Conserved Domains (2) summary
      sd00039
      Location:4787
      7WD40; WD40 repeat [structural motif]
      cl29593
      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_001278946.2NP_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/TrEMBL
      Q53GB2
      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
      A8MV37, B4DXJ1, P55735, Q5BJF0, Q9BRM6, Q9BUG7
      UniProtKB/TrEMBL
      Q53GB2
      Related
      ENSP00000312122.4, ENST00000350697.8
      Conserved Domains (2) summary
      sd00039
      Location:61101
      7WD40; WD40 repeat [structural motif]
      cl29593
      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: GCF_000001405.40-RS_2024_08

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000003.12 Reference GRCh38.p14 Primary Assembly

      Range
      10300931..10321112 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_017007021.2XP_016862510.1  protein SEC13 homolog isoform X8

      UniProtKB/TrEMBL
      A8MXL6
      Related
      ENSP00000380306.1, ENST00000397117.5
    2. XM_047448696.1XP_047304652.1  protein SEC13 homolog isoform X6

    3. XM_047448694.1XP_047304650.1  protein SEC13 homolog isoform X5

    4. XM_047448698.1XP_047304654.1  protein SEC13 homolog isoform X6

    5. XM_047448693.1XP_047304649.1  protein SEC13 homolog isoform X4

    6. XM_047448691.1XP_047304647.1  protein SEC13 homolog isoform X3

    7. XM_047448697.1XP_047304653.1  protein SEC13 homolog isoform X2

    8. XM_047448688.1XP_047304644.1  protein SEC13 homolog isoform X1

    9. XM_047448692.1XP_047304648.1  protein SEC13 homolog isoform X4

    10. XM_017007020.3XP_016862509.2  protein SEC13 homolog isoform X7

      UniProtKB/TrEMBL
      A8MXL6
      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 ...
    11. XM_047448690.1XP_047304646.1  protein SEC13 homolog isoform X3

    12. XM_047448689.1XP_047304645.1  protein SEC13 homolog isoform X2

    13. XM_047448687.1XP_047304643.1  protein SEC13 homolog isoform X1

    14. XM_047448695.1XP_047304651.1  protein SEC13 homolog isoform X5

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060927.1 Alternate T2T-CHM13v2.0

      Range
      10294231..10314421 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054347504.1XP_054203479.1  protein SEC13 homolog isoform X8

    2. XM_054347500.1XP_054203475.1  protein SEC13 homolog isoform X6

    3. XM_054347498.1XP_054203473.1  protein SEC13 homolog isoform X5

    4. XM_054347503.1XP_054203478.1  protein SEC13 homolog isoform X6

    5. XM_054347497.1XP_054203472.1  protein SEC13 homolog isoform X4

    6. XM_054347495.1XP_054203470.1  protein SEC13 homolog isoform X3

    7. XM_054347502.1XP_054203477.1  protein SEC13 homolog isoform X2

    8. XM_054347492.1XP_054203467.1  protein SEC13 homolog isoform X1

    9. XM_054347496.1XP_054203471.1  protein SEC13 homolog isoform X4

    10. XM_054347501.1XP_054203476.1  protein SEC13 homolog isoform X7

    11. XM_054347494.1XP_054203469.1  protein SEC13 homolog isoform X3

    12. XM_054347493.1XP_054203468.1  protein SEC13 homolog isoform X2

    13. XM_054347491.1XP_054203466.1  protein SEC13 homolog isoform X1

    14. XM_054347499.1XP_054203474.1  protein SEC13 homolog isoform X5