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

Gene ID: 9117, updated on 2-Nov-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
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Genomic context

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See SEC22C in Genome Data Viewer
Location:
3p22.1
Exon count:
12
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (42547969..42601078, complement)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (42565963..42619072, complement)
RS_2024_09 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 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. CFTR interactome mapping using the mammalian membrane two-hybrid high-throughput screening system. Lim SH, et al. Mol Syst Biol, 2022 Feb. PMID 35156780, Free PMC Article
  4. Widespread Expansion of Protein Interaction Capabilities by Alternative Splicing. Yang X, et al. Cell, 2016 Feb 11. PMID 26871637, Free PMC Article
  5. 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

See all (13) citations in PubMed

GeneRIFs: Gene References Into Functions

Phenotypes

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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_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
    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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