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    SEC22C SEC22 homolog C, vesicle trafficking protein [ Homo sapiens (human) ]

    Gene ID: 9117, updated on 3-Apr-2024

    Summary

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    Official Symbol
    SEC22Cprovided by HGNC
    Official Full Name
    SEC22 homolog C, vesicle trafficking proteinprovided by HGNC
    Primary source
    HGNC:HGNC:16828
    See related
    Ensembl:ENSG00000093183 MIM:604028; AllianceGenome:HGNC:16828
    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
    SEC22L3
    Summary
    This gene encodes a member of the SEC22 family of vesicle trafficking proteins. The encoded protein is localized to the endoplasmic reticulum and may play a role in the early stages of ER-Golgi protein trafficking. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. [provided by RefSeq, Jan 2011]
    Expression
    Ubiquitous expression in prostate (RPKM 10.0), bone marrow (RPKM 7.3) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    Location:
    3p22.1
    Exon count:
    12
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (42547969..42601078, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (42565963..42619072, complement)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (42589461..42642570, complement)

    Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124909372 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:42542633-42543206 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14243 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14244 Neighboring gene Sharpr-MPRA regulatory region 5178 Neighboring gene vasoactive intestinal peptide receptor 1 Neighboring gene ReSE screen-validated silencer GRCh37_chr3:42566136-42566306 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:42574871-42575372 Neighboring gene VIPR1 antisense RNA 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:42581415-42581916 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:42581917-42582416 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:42622926-42623752 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19746 Neighboring gene SS18 like 2 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14246 Neighboring gene ZBTB47 and NKTR antisense RNA 1 Neighboring gene natural killer cell triggering receptor Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr3:42672544-42673392 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr3:42673393-42674241 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19747 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19748 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:42695163-42695804 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14248 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14247 Neighboring gene Sharpr-MPRA regulatory region 3469 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:42700825-42701735 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:42701736-42702645 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19749 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:42706502-42707002 Neighboring gene uncharacterized LOC124906232 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:42708562-42709098 Neighboring gene zinc finger and BTB domain containing 47 Neighboring gene RNA, 7SL, cytoplasmic 567, pseudogene

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • 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

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    Related articles in PubMed

    1. The number of the C-terminal transmembrane domains has the potency to specify subcellular localization of Sec22c. Yamamoto Y, et al. Biochem Biophys Res Commun, 2017 May 27. PMID 28414125
    2. Hsec22c: a homolog of yeast Sec22p and mammalian rsec22a and msec22b/ERS-24. Tang BL, et al. Biochem Biophys Res Commun, 1998 Feb 24. PMID 9501016
    3. Widespread Expansion of Protein Interaction Capabilities by Alternative Splicing. Yang X, et al. Cell, 2016 Feb 11. PMID 26871637, Free PMC Article
    4. The secreted protein discovery initiative (SPDI), a large-scale effort to identify novel human secreted and transmembrane proteins: a bioinformatics assessment. Clark HF, et al. Genome Res, 2003 Oct. PMID 12975309, Free PMC Article
    5. A proteome-scale map of the human interactome network. Rolland T, et al. Cell, 2014 Nov 20. PMID 25416956, Free PMC Article

    See all (12) citations in PubMed

    GeneRIFs: Gene References Into Functions

    Phenotypes

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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Genotypes

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • MGC5373, MGC13261, DKFZp761F2321

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in endoplasmic reticulum to Golgi vesicle-mediated transport IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in protein transport IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    located_in endoplasmic reticulum TAS
    Traceable Author Statement
    more info
    		 PubMed 
    located_in endoplasmic reticulum membrane IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in membrane TAS
    Traceable Author Statement
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    vesicle-trafficking protein SEC22c
    Names
    SEC22 vesicle trafficking protein homolog C
    SEC22 vesicle trafficking protein-like 3
    SEC22 vesicle trafficking protein-like protein C
    secretion deficient 22C

    NCBI Reference Sequences (RefSeq)

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    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_001201572.2 → NP_001188501.1  vesicle-trafficking protein SEC22c isoform b

      See identical proteins and their annotated locations for NP_001188501.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) differs in the 5' and 3' UTRs and uses an alternate splice site in the 3' coding region, which results in a frameshift, compared to variant 1. The encoded isoform (b), is shorter and has a distinct C-terminus, compared to isoform a. Variants 2 and 3 encode the same isoform (b).
      Source sequence(s)
      BC018437, BX377531, CB410223, DA434403
      Consensus CDS
      CCDS2699.1
      UniProtKB/TrEMBL
      C9J448
      Related
      ENSP00000407564.1, ENST00000417572.5
      Conserved Domains (1) summary
      pfam13774
      Location:42 → 114
      Longin; Regulated-SNARE-like domain

    2. NM_001201584.2 → NP_001188513.1  vesicle-trafficking protein SEC22c isoform c

      See identical proteins and their annotated locations for NP_001188513.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) differs in the 3' UTR, lacks an exon in the 3' coding region and uses an alternate splice site in the 3' coding region, which results in a frameshift, compared to variant 1. The encoded isoform (c), is shorter and has a distinct C-terminus, compared to isoform a.
      Source sequence(s)
      AK074576, AY359041
      Consensus CDS
      CCDS56246.1
      UniProtKB/TrEMBL
      C9J448
      Related
      ENSP00000414576.2, ENST00000423701.6
      Conserved Domains (1) summary
      pfam13774
      Location:38 → 99
      Longin; Regulated-SNARE-like domain

    3. NM_004206.4 → NP_004197.1  vesicle-trafficking protein SEC22c isoform b

      See identical proteins and their annotated locations for NP_004197.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) differs in the 3' UTR and uses an alternate splice site in the 3' coding region, which results in a frameshift, compared to variant 1. The encoded isoform (b), is shorter and has a distinct C-terminus, compared to isoform a. Variants 2 and 3 encode the same isoform (b).
      Source sequence(s)
      AK074576, BC018437, CB410223
      Consensus CDS
      CCDS2699.1
      UniProtKB/TrEMBL
      C9J448
      Related
      ENSP00000273156.7, ENST00000273156.11
      Conserved Domains (1) summary
      pfam13774
      Location:42 → 114
      Longin; Regulated-SNARE-like domain

    4. NM_032970.4 → NP_116752.1  vesicle-trafficking protein SEC22c isoform a

      See identical proteins and their annotated locations for NP_116752.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (a).
      Source sequence(s)
      AC092047, AK074576, BC006178, CB410223
      Consensus CDS
      CCDS2700.1
      UniProtKB/Swiss-Prot
      O95152, Q68CX3, Q6UW18, Q9BRL7
      UniProtKB/TrEMBL
      A0A024R2N5, A0A0S2Z4S0, A0A0S2Z4U4
      Related
      ENSP00000264454.3, ENST00000264454.8
      Conserved Domains (1) summary
      pfam13774
      Location:42 → 114
      Longin; Regulated-SNARE-like domain

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

    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
      42547969..42601078 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047449170.1 → XP_047305126.1  vesicle-trafficking protein SEC22c isoform X2

    2. XM_047449168.1 → XP_047305124.1  vesicle-trafficking protein SEC22c isoform X1

      UniProtKB/Swiss-Prot
      O95152, Q68CX3, Q6UW18, Q9BRL7
      UniProtKB/TrEMBL
      A0A024R2N5, A0A0S2Z4U4

    3. XM_024453814.2 → XP_024309582.1  vesicle-trafficking protein SEC22c isoform X2

      UniProtKB/TrEMBL
      C9J448
      Related
      ENSP00000391170.1, ENST00000456515.5
      Conserved Domains (1) summary
      pfam13774
      Location:42 → 114
      Longin; Regulated-SNARE-like domain

    4. XM_024453812.2 → XP_024309580.1  vesicle-trafficking protein SEC22c isoform X1

      UniProtKB/Swiss-Prot
      O95152, Q68CX3, Q6UW18, Q9BRL7
      UniProtKB/TrEMBL
      A0A024R2N5, A0A0S2Z4S0, A0A0S2Z4U4
      Conserved Domains (1) summary
      pfam13774
      Location:42 → 114
      Longin; Regulated-SNARE-like domain

    5. XM_047449169.1 → XP_047305125.1  vesicle-trafficking protein SEC22c isoform X2

    6. XM_011534212.3 → XP_011532514.1  vesicle-trafficking protein SEC22c isoform X1

      See identical proteins and their annotated locations for XP_011532514.1

      UniProtKB/Swiss-Prot
      O95152, Q68CX3, Q6UW18, Q9BRL7
      UniProtKB/TrEMBL
      A0A024R2N5, A0A0S2Z4S0, A0A0S2Z4U4
      Conserved Domains (1) summary
      pfam13774
      Location:42 → 114
      Longin; Regulated-SNARE-like domain

    7. XM_047449171.1 → XP_047305127.1  vesicle-trafficking protein SEC22c isoform X3

      Related
      ENSP00000415969.1, ENST00000451653.5

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060927.1 Alternate T2T-CHM13v2.0

      Range
      42565963..42619072 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054348333.1 → XP_054204308.1  vesicle-trafficking protein SEC22c isoform X2

    2. XM_054348330.1 → XP_054204305.1  vesicle-trafficking protein SEC22c isoform X1

      UniProtKB/Swiss-Prot
      O95152, Q68CX3, Q6UW18, Q9BRL7
      UniProtKB/TrEMBL
      A0A024R2N5, A0A0S2Z4U4

    3. XM_054348331.1 → XP_054204306.1  vesicle-trafficking protein SEC22c isoform X2

    4. XM_054348328.1 → XP_054204303.1  vesicle-trafficking protein SEC22c isoform X1

      UniProtKB/Swiss-Prot
      O95152, Q68CX3, Q6UW18, Q9BRL7
      UniProtKB/TrEMBL
      A0A024R2N5, A0A0S2Z4U4

    5. XM_054348332.1 → XP_054204307.1  vesicle-trafficking protein SEC22c isoform X2

    6. XM_054348329.1 → XP_054204304.1  vesicle-trafficking protein SEC22c isoform X1

      UniProtKB/Swiss-Prot
      O95152, Q68CX3, Q6UW18, Q9BRL7
      UniProtKB/TrEMBL
      A0A024R2N5, A0A0S2Z4U4

    7. XM_054348334.1 → XP_054204309.1  vesicle-trafficking protein SEC22c isoform X3

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9BRL7.1 GenPept UniProtKB/Swiss-Prot:Q9BRL7

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