SEC23IP SEC23 interacting protein [Homo sapiens (human)] - Gene

Summary

Official Symbol: SEC23IPprovided by HGNC
Official Full Name: SEC23 interacting proteinprovided by HGNC
Primary source: HGNC:HGNC:17018
See related: Ensembl:ENSG00000107651 MIM:617852; AllianceGenome:HGNC:17018
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: P125; P125A; iPLA1A; MSTP053; iPLA1beta
Summary: This gene encodes a member of the phosphatidic acid preferring-phospholipase A1 family. The encoded protein is localized to endoplasmic reticulum exit sites and plays a critical role in ER-Golgi transport as part of the multimeric coat protein II complex. An orthologous gene in frogs is required for normal neural crest cell development, suggesting that this gene may play a role in Waardenburg syndrome neural crest defects. Alternatively spliced transcript variants have been observed for this gene. [provided by RefSeq, Feb 2011]
Expression: Ubiquitous expression in thyroid (RPKM 7.9), stomach (RPKM 7.7) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 10q26.11-q26.12

Exon count:: 20

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	10	NC_000010.11 (119892730..119944657)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	10	NC_060934.1 (120790271..120842184)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	10	NC_000010.10 (121652242..121704169)

Chromosome 10 - NC_000010.11 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 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?

Sec23IP recruits VPS13B/COH1 to ER exit site-Golgi interface for tubular ERGIC formation.
Title: Sec23IP recruits VPS13B/COH1 to ER exit site-Golgi interface for tubular ERGIC formation.
A basic cluster and a hydrophobic interface in the DDHD and SAM domains, respectively, are required for p125A-mediated functional endoplasmic reticulum exit site assembly.
Title: A cascade of ER exit site assembly that is regulated by p125A and lipid signals.
Xenopus sec23ip is required for normal neural crest cell development, suggesting a role for the human ortholog in Waardenburg syndrome neural crest defects.
Title: Systematic discovery of nonobvious human disease models through orthologous phenotypes.
The results suggest that p125A is part of the Sec13/Sec31A subcomplex and facilitates ER export in mammalian cells.
Title: p125A exists as part of the mammalian Sec13/Sec31 COPII subcomplex to facilitate ER-Golgi transport.
Observational study of gene-disease association. (HuGE Navigator)
Title: Coeliac disease-associated risk variants in TNFAIP3 and REL implicate altered NF-kappaB signalling.
p125 is a mammalian-specific component of ER exit sites and participates in the organization of this compartment
Title: p125 is localized in endoplasmic reticulum exit sites and involved in their organization.

Submit: New GeneRIF Correction

Phenotypes

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Review eQTL and phenotype association data in this region using PheGenI

EBI GWAS Catalog

Description
Parent-of-origin-specific allelic associations among 106 genomic loci for age at menarche. EBI GWAS Catalog EBI GWAS CatalogPubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

RH44608 (e-PCR)
- UniSTS:43812

STS-H95966 (e-PCR)
- UniSTS:26165

A009L28 (e-PCR)
- UniSTS:15980

RH36905 (e-PCR)
- UniSTS:87932

STS-N22197 (e-PCR)
- UniSTS:82365

G32653 (e-PCR)
- UniSTS:117235

RH103201 (e-PCR)
- UniSTS:97534

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables RNA binding	HDA more info	PubMed
enables metal ion binding	IEA Inferred from Electronic Annotation more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in Golgi organization	TAS Traceable Author Statement more info	PubMed
involved_in endoplasmic reticulum to Golgi vesicle-mediated transport	IEA Inferred from Electronic Annotation more info
involved_in intracellular protein transport	TAS Traceable Author Statement more info	PubMed

Component	Evidence Code	Pubs
is_active_in COPII-coated ER to Golgi transport vesicle	IBA Inferred from Biological aspect of Ancestor more info
located_in COPII-coated ER to Golgi transport vesicle	TAS Traceable Author Statement more info
located_in ER to Golgi transport vesicle membrane	IEA Inferred from Electronic Annotation more info
located_in Golgi apparatus	IDA Inferred from Direct Assay more info
located_in cytoplasm	TAS Traceable Author Statement more info	PubMed
located_in cytosol	TAS Traceable Author Statement more info
located_in endoplasmic reticulum	IEA Inferred from Electronic Annotation more info
located_in endoplasmic reticulum-Golgi intermediate compartment	TAS Traceable Author Statement more info	PubMed
located_in intracellular membrane-bounded organelle	IDA Inferred from Direct Assay more info

General protein information

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Preferred Names: SEC23-interacting protein

Names: intracellular phospholipase A1 beta

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_001411070.1 → NP_001397999.1 SEC23-interacting protein isoform 2

Status: REVIEWED

Source sequence(s)

AC027672

Consensus CDS

CCDS91362.1

UniProtKB/TrEMBL

A0A994J542

Related

ENSP00000516127.1, ENST00000705471.1
NM_007190.4 → NP_009121.1 SEC23-interacting protein isoform 1

See identical proteins and their annotated locations for NP_009121.1

Status: REVIEWED

Description

Transcript Variant: This variant (1) represents the longer transcript and encodes a functional protein.

Source sequence(s)

AB019435, AC027672, AI093198, BC063800

Consensus CDS

CCDS7618.1

UniProtKB/Swiss-Prot

D3DRD2, Q8IXH5, Q9BUK5, Q9Y6Y8

UniProtKB/TrEMBL

B3KM47

Related

ENSP00000358071.3, ENST00000369075.8

Conserved Domains (3) summary

cd09584
Location:638 → 702

SAM_sec23ip; SAM domain of sec23ip

smart00454
Location:641 → 701

SAM; Sterile alpha motif

pfam02862
Location:782 → 988

DDHD; DDHD domain

RNA

NR_037771.2 RNA Sequence

Status: REVIEWED

Description

Transcript Variant: This variant (2) lacks an internal exon, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).

Source sequence(s)

AC027672, AI093198, AK301517, BC063800, DA942854