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

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: mouse all
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Genomic context

Location:: 3p25.3

Exon count:: 12

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	3	NC_000003.12 (10300931..10321112, complement)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	3	NC_060927.1 (10294231..10314421, complement)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	3	NC_000003.11 (10342615..10362796, complement)

Chromosome 3 - NC_000003.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

TRAPPC12, but not TRAPPC8, bound to Sec13/Sec31A tetramer but each Sec protein alone could not interact with TRAPPC12.
Title: Mammalian TRAPPIII Complex positively modulates the recruitment of Sec13/31 onto COPII vesicles.
we demonstrated Sec13 as a novel component that was involved in VISA-mediated antiviral signaling pathway.
Title: Sec13 is a positive regulator of VISA-mediated antiviral signaling.
GNL2 and SEC13 are required for nonsense-mediated mRNA decay pathway in human cells.
Title: Identification and characterization of novel factors that act in the nonsense-mediated mRNA decay pathway in nematodes, flies and mammals.
When embedded in a three-dimensional matrix, Sec13-depleted Caco-2 cells form cysts but, unlike controls, are defective in lumen expansion.
Title: Epithelial organization and cyst lumen expansion require efficient Sec13-Sec31-driven secretion.
The identified Sec13 interaction to PS1 is a new candidate interaction for linking PS1 to secretory and protein degrading vesicular circuits.
Title: The coat protein complex II, COPII, protein Sec13 directly interacts with presenilin-1.
Data show that coupling of the Sec23/24 and Sec13/31 layers of the COPII coat is required to drive export of collagen from the endoplasmic reticulum, and that efficient COPII assembly is essential for normal craniofacial development during embryogenesis.
Title: Efficient coupling of Sec23-Sec24 to Sec13-Sec31 drives COPII-dependent collagen secretion and is essential for normal craniofacial development.
Determine crystal structure of Sec13-Nup145C dimer.
Title: Architecture of a coat for the nuclear pore membrane.
three-dimensional reconstruction of Sec13/31 cages at 30 A resolution using cryo-electron microscopy and single particle analysis
Title: Structure of the Sec13/31 COPII coat cage.

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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)

HIV-1 interactions

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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

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

D3S2866E (e-PCR)
- UniSTS:150875

GDB:186267 (e-PCR)
- UniSTS:155483

D15S1477 (e-PCR)
- UniSTS:474482

T15986 (e-PCR)
- UniSTS:40104

D3S1350 (e-PCR)
- UniSTS:147895

SHGC-2675 (e-PCR)
- UniSTS:91075

SHGC-2687 (e-PCR)
- UniSTS:91076

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 TOR signaling	IMP Inferred from Mutant Phenotype more info	PubMed
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 more info	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

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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)

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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)

NM_001136026.3 → NP_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:107 → 147

7WD40; WD40 repeat [structural motif]

cl25539
Location:56 → 335

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 ...
NM_001136232.3 → NP_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:47 → 87

7WD40; WD40 repeat [structural motif]

cl29593
Location:11 → 275

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 ...
NM_001278946.2 → NP_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:24 → 155

WD40; WD40 repeat [General function prediction only]

sd00039
Location:61 → 101

7WD40; WD40 repeat [structural motif]

cl02567
Location:25 → 129

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 ...
NM_030673.4 → NP_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:9 → 304

WD40; WD40 repeat [General function prediction only]

sd00039
Location:64 → 104

7WD40; WD40 repeat [structural motif]

cl02567
Location:13 → 292

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 ...
NM_183352.3 → NP_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:61 → 101

7WD40; WD40 repeat [structural motif]

cl29593
Location:10 → 289

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_2023_10

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

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000003.12 Reference GRCh38.p14 Primary Assembly

Range

10300931..10321112 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

UniProtKB/TrEMBL

A8MXL6

Related

ENSP00000380306.1, ENST00000397117.5
XM_047448696.1 → XP_047304652.1 protein SEC13 homolog isoform X6
XM_047448694.1 → XP_047304650.1 protein SEC13 homolog isoform X5
XM_047448698.1 → XP_047304654.1 protein SEC13 homolog isoform X6
XM_047448693.1 → XP_047304649.1 protein SEC13 homolog isoform X4
XM_047448691.1 → XP_047304647.1 protein SEC13 homolog isoform X3
XM_047448697.1 → XP_047304653.1 protein SEC13 homolog isoform X2
XM_047448688.1 → XP_047304644.1 protein SEC13 homolog isoform X1
XM_047448692.1 → XP_047304648.1 protein SEC13 homolog isoform X4
XM_017007020.3 → XP_016862509.2 protein SEC13 homolog isoform X7

UniProtKB/TrEMBL

A8MXL6

Conserved Domains (2) summary

sd00039
Location:79 → 119

7WD40; WD40 repeat [structural motif]

cl25539
Location:28 → 303

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 ...
XM_047448690.1 → XP_047304646.1 protein SEC13 homolog isoform X3
XM_047448689.1 → XP_047304645.1 protein SEC13 homolog isoform X2
XM_047448687.1 → XP_047304643.1 protein SEC13 homolog isoform X1
XM_047448695.1 → XP_047304651.1 protein SEC13 homolog isoform X5