Sec24a SEC24 homolog A, COPII coat complex component [Mus musculus (house mouse)] - Gene

Summary

Official Symbol: Sec24aprovided by MGI
Official Full Name: SEC24 homolog A, COPII coat complex componentprovided by MGI
Primary source: MGI:MGI:1924621
See related: Ensembl:ENSMUSG00000036391 AllianceGenome:MGI:1924621
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Mus musculus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Summary: Predicted to enable SNARE binding activity and zinc ion binding activity. Acts upstream of or within cholesterol homeostasis; positive regulation of protein secretion; and regulation of cholesterol transport. Predicted to be located in cytoplasmic vesicle; endoplasmic reticulum; and membrane. Predicted to be part of COPII vesicle coat. Predicted to be active in endoplasmic reticulum exit site. Is expressed in embryo. Orthologous to human SEC24A (SEC24 homolog A, COPII coat complex component). [provided by Alliance of Genome Resources, Apr 2022]
Expression: Ubiquitous expression in small intestine adult (RPKM 7.6), liver adult (RPKM 6.9) and 28 other tissues See more
Orthologs: human all
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Genomic context

Location:: 11 B1.3; 11 31.28 cM

Exon count:: 24

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCm39 (GCF_000001635.27)	11	NC_000077.7 (51583090..51649172, complement)
108.20200622	previous assembly	GRCm38.p6 (GCF_000001635.26)	11	NC_000077.6 (51692263..51757161, complement)

Chromosome 11 - NC_000077.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

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Expression

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See details

Project title: Mouse ENCODE transcriptome data
Description: RNA profiling data sets generated by the Mouse ENCODE project.
BioProject: PRJNA66167
Publication: PMID 25409824
Analysis date: n/a

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Hepatic LDLR levels are up-regulated in SEC24A-deficient cells as a consequence of specific dependence of PCSK9, a negative regulator of LDLR, on SEC24A for efficient exit from the ensoplasmic reticulum.
Title: SEC24A deficiency lowers plasma cholesterol through reduced PCSK9 secretion.

Submit: New GeneRIF Correction

Variation

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Alleles

Alleles of this type are documented at Mouse Genome Informatics (MGI)

Gene trapped (1)
Targeted (3) 1 citation
Endonuclease-mediated (1)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

RH126541 (e-PCR)
- UniSTS:208675

AI504915 (e-PCR)
- UniSTS:160093

NoName (e-PCR)
- UniSTS:488956

Gene Ontology Provided by MGI

Function	Evidence Code	Pubs
enables SNARE binding	IBA Inferred from Biological aspect of Ancestor more info
enables metal ion binding	IEA Inferred from Electronic Annotation more info
enables zinc ion binding	IBA Inferred from Biological aspect of Ancestor more info
enables zinc ion binding	ISO Inferred from Sequence Orthology more info

Process	Evidence Code	Pubs
involved_in COPII-coated vesicle cargo loading	IBA Inferred from Biological aspect of Ancestor more info
involved_in COPII-coated vesicle cargo loading	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within cholesterol homeostasis	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in endoplasmic reticulum to Golgi vesicle-mediated transport	ISO Inferred from Sequence Orthology more info
involved_in intracellular protein transport	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within positive regulation of protein secretion	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within protein transport	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within regulation of cholesterol transport	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within vesicle-mediated transport	IEA Inferred from Electronic Annotation 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	ISO Inferred from Sequence Orthology more info
located_in cytoplasm	IEA Inferred from Electronic Annotation more info
located_in cytoplasmic vesicle	IEA Inferred from Electronic Annotation more info
located_in endoplasmic reticulum	IEA Inferred from Electronic Annotation more info
is_active_in endoplasmic reticulum exit site	IBA Inferred from Biological aspect of Ancestor more info
located_in membrane	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: protein transport protein Sec24A

Names: SEC24-related protein A; Sec24 related gene family, member A

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_001290785.1 → NP_001277714.1 protein transport protein Sec24A isoform 2

Status: VALIDATED

Description

Transcript Variant: This variant (2) uses an alternate in-frame splice site in the central coding region, compared to variant 1. The encoded isoform (2) is shorter, compared to isoform 1.

Source sequence(s)

AK029139, AK163254, AL645602, BC096594

Consensus CDS

CCDS70181.1

UniProtKB/TrEMBL

A2AA71

Related

ENSMUSP00000044370.6, ENSMUST00000038210.12

Conserved Domains (6) summary

cd01479
Location:497 → 739

Sec24-like; Sec24-like: Protein and membrane traffic in eukaryotes is mediated by at least in part by the budding and fusion of intracellular transport vesicles that selectively carry cargo proteins and lipids from donor to acceptor organelles. The two main classes ...

pfam00626
Location:960 → 1035

Gelsolin; Gelsolin repeat

pfam04503
Location:7 → 177

SSDP; Single-stranded DNA binding protein, SSDP

pfam04810
Location:424 → 460

zf-Sec23_Sec24; Sec23/Sec24 zinc finger

pfam04815
Location:839 → 934

Sec23_helical; Sec23/Sec24 helical domain

pfam08033
Location:740 → 824

Sec23_BS; Sec23/Sec24 beta-sandwich domain
NM_175255.3 → NP_780464.2 protein transport protein Sec24A isoform 1

See identical proteins and their annotated locations for NP_780464.2

Status: VALIDATED

Description

Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).

Source sequence(s)

AK029139, AK163254, AL645602, BG065014, CJ055291

Consensus CDS

CCDS24660.2

UniProtKB/Swiss-Prot

A2AA70, A2AA73, A4FUV4, Q3TQ05, Q3TRG7, Q3U2P1, Q8BIS0

Related

ENSMUSP00000104725.3, ENSMUST00000109097.9

Conserved Domains (6) summary

cd01479
Location:498 → 740

Sec24-like; Sec24-like: Protein and membrane traffic in eukaryotes is mediated by at least in part by the budding and fusion of intracellular transport vesicles that selectively carry cargo proteins and lipids from donor to acceptor organelles. The two main classes ...

pfam00626
Location:961 → 1036

Gelsolin; Gelsolin repeat

pfam04503
Location:7 → 177

SSDP; Single-stranded DNA binding protein, SSDP

pfam04810
Location:425 → 461

zf-Sec23_Sec24; Sec23/Sec24 zinc finger

pfam04815
Location:840 → 935

Sec23_helical; Sec23/Sec24 helical domain

pfam08033
Location:741 → 825

Sec23_BS; Sec23/Sec24 beta-sandwich domain

RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

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

Reference GRCm39 C57BL/6J

Genomic

NC_000077.7 Reference GRCm39 C57BL/6J

Range

51583090..51649172 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_017314833.3 → XP_017170322.1 protein transport protein Sec24A isoform X1

UniProtKB/TrEMBL

A2AA72

Related

ENSMUSP00000068065.5, ENSMUST00000064297.5

Conserved Domains (2) summary

PHA03247
Location:5 → 367

PHA03247; large tegument protein UL36; Provisional

COG5028
Location:297 → 589

COG5028; Vesicle coat complex COPII, subunit SEC24/subunit SFB2/subunit SFB3 [Intracellular trafficking and secretion]