Scfd1 sec1 family domain containing 1 [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Scfd1provided by RGD
Official Full Name: sec1 family domain containing 1provided by RGD
Primary source: RGD:619828
See related: EnsemblRapid:ENSRNOG00000031203 AllianceGenome:RGD:619828
Gene type: protein coding
RefSeq status: PROVISIONAL
Organism: Rattus norvegicus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Also known as: Sly1; RA410; rSly1
Summary: Enables syntaxin binding activity. Involved in Golgi vesicle transport; regulation of ER to Golgi vesicle-mediated transport; and response to hypoxia. Located in Golgi-associated vesicle. Orthologous to human SCFD1 (sec1 family domain containing 1). [provided by Alliance of Genome Resources, Dec 2024]
Expression: Biased expression in Kidney (RPKM 171.9), Liver (RPKM 171.0) and 9 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 6q22

Exon count:: 24

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	6	NC_086024.1 (74531225..74609463)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	6	NC_051341.1 (68795810..68874076)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	6	NC_005105.4 (72124408..72202703)

Chromosome 6 - NC_086024.1 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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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?

These results suggest that RA410/Sly1 plays an important cytoprotective role in MPP+ and 6-OHDA-induced cellular perturbation.
Title: RA410/Sly1 suppresses MPP+ and 6-hydroxydopamine-induced cell death in SH-SY5Y cells.
elucidated the structure in solution of the isolated N-terminal domain of rat Sly1 and analyzed its complex with an N-terminal peptide of rat syntaxin 5 by NMR spectroscopy
Title: Three-dimensional structure of the rSly1 N-terminal domain reveals a conformational change induced by binding to syntaxin 5.
results argue that although rsly1 does not seem to regulate the availability of syntaxin 5, its function is intimately associated with syntaxin binding, perhaps promoting a later step in SNARE complex formation or function
Title: rsly1 binding to syntaxin 5 is required for endoplasmic reticulum-to-Golgi transport but does not promote SNARE motif accessibility.

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Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein-containing complex binding	IDA Inferred from Direct Assay more info	PubMed
enables syntaxin binding	IBA Inferred from Biological aspect of Ancestor more info
enables syntaxin binding	IDA Inferred from Direct Assay more info	PubMed
enables syntaxin binding	IPI Inferred from Physical Interaction more info	PubMed
enables syntaxin binding	TAS Traceable Author Statement more info	PubMed

Process	Evidence Code	Pubs
involved_in cell morphogenesis	ISS Inferred from Sequence or Structural Similarity more info
involved_in endoplasmic reticulum to Golgi vesicle-mediated transport	IBA Inferred from Biological aspect of Ancestor more info
involved_in endoplasmic reticulum to Golgi vesicle-mediated transport	TAS Traceable Author Statement more info	PubMed
involved_in intracellular protein transport	IBA Inferred from Biological aspect of Ancestor more info
involved_in negative regulation of autophagosome assembly	ISO Inferred from Sequence Orthology more info
involved_in post-Golgi vesicle-mediated transport	IDA Inferred from Direct Assay more info	PubMed
involved_in protein transport	IEA Inferred from Electronic Annotation more info
involved_in regulation of ER to Golgi vesicle-mediated transport	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of protein transport	ISO Inferred from Sequence Orthology more info
involved_in response to hypoxia	IEP Inferred from Expression Pattern more info	PubMed
involved_in response to toxic substance	ISO Inferred from Sequence Orthology more info
involved_in retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum	IBA Inferred from Biological aspect of Ancestor more info
involved_in retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in vesicle-mediated transport	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
located_in Golgi cisterna membrane	IEA Inferred from Electronic Annotation more info
is_active_in Golgi membrane	IBA Inferred from Biological aspect of Ancestor more info
located_in Golgi-associated vesicle	IDA Inferred from Direct Assay more info	PubMed
located_in cis-Golgi network	ISO Inferred from Sequence Orthology more info
located_in endoplasmic reticulum membrane	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: sec1 family domain-containing protein 1

Names: SLY1 homolog; sly1p; syntaxin-binding protein 1-like 2; vesicle transport-related protein Ra410

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_019364.1 → NP_062237.1 sec1 family domain-containing protein 1

See identical proteins and their annotated locations for NP_062237.1

Status: PROVISIONAL

Source sequence(s)

D79221

UniProtKB/Swiss-Prot

Q62843, Q62991

UniProtKB/TrEMBL

A0A8I6AGF5, A6HBG9

Related

ENSRNOP00000039132.1, ENSRNOT00000040548.4

Conserved Domains (1) summary

pfam00995
Location:39 → 457

Sec1; Sec1 family

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_086024.1 Reference GRCr8

Range

74531225..74609463

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_006240085.5 → XP_006240147.1 sec1 family domain-containing protein 1 isoform X1

UniProtKB/TrEMBL

A0A8I5Y1I7

Conserved Domains (1) summary

pfam00995
Location:39 → 457

Sec1; Sec1 family