Sec24d SEC24 homolog D, COPII coat complex component [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Sec24dprovided by RGD
Official Full Name: SEC24 homolog D, COPII coat complex componentprovided by RGD
Primary source: RGD:1311720
See related: Ensembl:ENSRNOG00000014872 AllianceGenome:RGD:1311720
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Rattus norvegicus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Summary: Predicted to enable SNARE binding activity and zinc ion binding activity. Predicted to be involved in COPII-coated vesicle cargo loading. Predicted to act upstream of or within in utero embryonic development. Predicted to be located in intracellular membrane-bounded organelle. Predicted to be part of COPII vesicle coat. Predicted to be active in endoplasmic reticulum exit site. Human ortholog(s) of this gene implicated in Cole-Carpenter syndrome. Orthologous to human SEC24D (SEC24 homolog D, COPII coat complex component). [provided by Alliance of Genome Resources, Apr 2022]
Expression: Biased expression in Heart (RPKM 137.5), Liver (RPKM 133.3) and 9 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 2q42

Exon count:: 23

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	2	NC_086020.1 (214103138..214211155)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	2	NC_051337.1 (211418557..211526588)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	2	NC_005101.4 (227455704..227562801)

Chromosome 2 - NC_086020.1 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: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
BioProject: PRJNA238328
Publication: PMID 24510058
Analysis date: Mon Jun 6 17:44:12 2016

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Sec24D expression is upregulated via CREB3L2 during hepatic stellate cells activation. Sec24D knockdown abrogated the activation.
Title: CREB3L2-mediated expression of Sec23A/Sec24D is involved in hepatic stellate cell activation through ER-Golgi transport.

Submit: New GeneRIF Correction

General gene information

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Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables SNARE binding	IBA Inferred from Biological aspect of Ancestor more info
enables SNARE binding	ISO Inferred from Sequence Orthology 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
involved_in endoplasmic reticulum to Golgi vesicle-mediated transport	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within in utero embryonic development	ISO Inferred from Sequence Orthology more info
involved_in intracellular protein 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 cytosol	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 endoplasmic reticulum membrane	IEA Inferred from Electronic Annotation more info
located_in intracellular membrane-bounded organelle	ISO Inferred from Sequence Orthology more info

General protein information

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Preferred Names: protein transport protein Sec24D

Names: SEC24 family member D; SEC24 related gene family, member D

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_001309453.1 → NP_001296382.1 protein transport protein Sec24D

See identical proteins and their annotated locations for NP_001296382.1

Status: VALIDATED

Source sequence(s)

BC168946, JAXUCZ010000002

UniProtKB/TrEMBL

A6HVI6, B5DF68, G3V9S9

Related

ENSRNOP00000059031.4, ENSRNOT00000064809.4

Conserved Domains (6) summary

COG5028
Location:217 → 1029

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

cd01479
Location:439 → 698

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:904 → 976

Gelsolin; Gelsolin repeat

pfam04810
Location:362 → 399

zf-Sec23_Sec24; Sec23/Sec24 zinc finger

pfam04815
Location:787 → 883

Sec23_helical; Sec23/Sec24 helical domain

pfam08033
Location:688 → 772

Sec23_BS; Sec23/Sec24 beta-sandwich domain

RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

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

Reference GRCr8

Genomic

NC_086020.1 Reference GRCr8

Range

214103138..214211155

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_006233272.5 → XP_006233334.1 protein transport protein Sec24D isoform X1

See identical proteins and their annotated locations for XP_006233334.1

UniProtKB/TrEMBL

G3V9S9

Conserved Domains (6) summary

COG5028
Location:180 → 1028

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

cd01479
Location:438 → 697

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:903 → 975

Gelsolin; Gelsolin repeat

pfam04810
Location:361 → 398

zf-Sec23_Sec24; Sec23/Sec24 zinc finger

pfam04815
Location:786 → 882

Sec23_helical; Sec23/Sec24 helical domain

pfam08033
Location:687 → 771

Sec23_BS; Sec23/Sec24 beta-sandwich domain

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

NM_001107723.1: Suppressed sequence

Description

NM_001107723.1: This RefSeq was removed because currently there is insufficient support for the transcript and the protein.