sec13 SEC13 homolog, nuclear pore and COPII coat complex component [Danio rerio (zebrafish)] - Gene

Summary

Official Symbol: sec13provided by ZNC
Official Full Name: SEC13 homolog, nuclear pore and COPII coat complex componentprovided by ZNC
Primary source: ZFIN:ZDB-GENE-040426-2649
See related: Ensembl:ENSDARG00000054807 AllianceGenome:ZFIN:ZDB-GENE-040426-2649
Gene type: protein coding
RefSeq status: PROVISIONAL
Organism: Danio rerio
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes; Danionidae; Danioninae; Danio
Also known as: cb271; sec13l1; sb:cb271; zgc:63980; wu:fa08f09
Summary: Predicted to enable structural molecule activity. Acts upstream of or within several processes, including animal organ development; extracellular matrix constituent secretion; and opsin transport. Located in endoplasmic reticulum exit site. Is expressed in several structures, including alar plate midbrain region; digestive system; optic vesicle; pectoral fin musculature; and skeletal element. Orthologous to human SEC13 (SEC13 homolog, nuclear pore and COPII coat complex component). [provided by Alliance of Genome Resources, Apr 2022]
Orthologs: human mouse all
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Genomic context

Location:: chromosome: 22

Exon count:: 9

Annotation release	Status	Assembly	Chr	Location
106	current	GRCz11 (GCF_000002035.6)	22	NC_007133.7 (31059975..31083488)
105	previous assembly	GRCz10 (GCF_000002035.5)	22	NC_007133.6 (31110780..31134293)

Chromosome 22 - NC_007133.7 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: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
Description: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
BioProject: PRJEB1986
Analysis date: Fri Dec 8 19:48:10 2017

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

suppression of the outer layer COPII component, Sec13, in embryos results in a disorganized gut epithelium
Title: Epithelial organization and cyst lumen expansion require efficient Sec13-Sec31-driven secretion.
A mutant gene encodes a carboxyl-terminus-truncated Sec13 that loses its affinity to Sec31a, which leads to disintegration of the ER structure in various differentiated cells.
Title: Sec13 safeguards the integrity of the endoplasmic reticulum and organogenesis of the digestive system in zebrafish.
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.

Submit: New GeneRIF Correction

General gene information

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Markers

AA542654 (e-PCR)
- UniSTS:206917

fc09d02.y1 (e-PCR)
- UniSTS:192386

fk34c03.y1 (e-PCR)
- UniSTS:200863

fk88f02.x1 (e-PCR)
- UniSTS:201667

Gene Ontology Provided by ZFIN

Function	Evidence Code	Pubs
enables structural molecule activity	IBA Inferred from Biological aspect of Ancestor more info
enables structural molecule activity	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
involved_in COPII-coated vesicle budding	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within cartilage development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within digestive system development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within endoplasmic reticulum organization	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within endoplasmic reticulum to Golgi vesicle-mediated transport	ISS Inferred from Sequence or Structural Similarity more info	PubMed
acts_upstream_of_or_within extracellular matrix constituent secretion	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within eye photoreceptor cell development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within liver development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within mRNA transport	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within opsin transport	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of TOR signaling	IBA Inferred from Biological aspect of Ancestor more info
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
acts_upstream_of_or_within protein transport	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within retina layer formation	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
part_of COPII vesicle coat	IBA Inferred from Biological aspect of Ancestor more info
located_in endoplasmic reticulum exit site	IDA Inferred from Direct Assay more info	PubMed
located_in lysosomal membrane	IEA Inferred from Electronic Annotation more info
located_in lysosome	IEA Inferred from Electronic Annotation more info
part_of nuclear pore	IEA Inferred from Electronic Annotation more info
part_of nuclear pore outer ring	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleus	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: protein SEC13 homolog

Names: SEC13 homolog, nuclear pore and COPII coating complex component; SEC13-like 1

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_213335.1 → NP_998500.1 protein SEC13 homolog

See identical proteins and their annotated locations for NP_998500.1

Status: PROVISIONAL

Source sequence(s)

BC054585

UniProtKB/TrEMBL

A8E568, Q7T2E1

Related

ENSDARP00000071531.5, ENSDART00000077063.6

Conserved Domains (3) summary

COG2319
Location:6 → 300

WD40; WD40 repeat [General function prediction only]

sd00039
Location:61 → 101

7WD40; WD40 repeat [structural motif]

cl02567
Location:7 → 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 ...