Sdf4 stromal cell derived factor 4 [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Sdf4provided by RGD
Official Full Name: stromal cell derived factor 4provided by RGD
Primary source: RGD:621521
See related: Ensembl:ENSRNOG00000019981 AllianceGenome:RGD:621521
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
Summary: Enables identical protein binding activity. Involved in several processes, including UV protection; response to ethanol; and zymogen granule exocytosis. Located in late endosome. Colocalizes with plasma membrane. Orthologous to human SDF4 (stromal cell derived factor 4). [provided by Alliance of Genome Resources, Apr 2022]
Expression: Biased expression in Liver (RPKM 871.0), Adrenal (RPKM 754.9) and 9 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 5q36

Exon count:: 10

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	5	NC_086023.1 (171868591..171885827)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	5	NC_051340.1 (166586581..166606661)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	5	NC_005104.4 (173425922..173444478)

Chromosome 5 - NC_086023.1 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?

The results suggest a mechanism for Cab45b action that involves regulating the dynamic association of Munc18b with SNAREs to impact beta-cell granule exocytosis.
Title: Cab45b, a Munc18b-interacting partner, regulates exocytosis in pancreatic beta-cells.
In a yeast two-hybrid screen the EF-hand Ca(2+)-binding protein Cab45 was identified as an interaction partner of Munc18b.
Title: A cytosolic splice variant of Cab45 interacts with Munc18b and impacts on amylase secretion by pancreatic acini.

Submit: New GeneRIF Correction

General gene information

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Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables calcium ion binding	IBA Inferred from Biological aspect of Ancestor more info
enables calcium ion binding	IEA Inferred from Electronic Annotation more info
enables calcium ion binding	ISO Inferred from Sequence Orthology more info
enables calcium ion binding	ISS Inferred from Sequence or Structural Similarity more info
enables identical protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in UV protection	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in calcium-ion regulated exocytosis	IBA Inferred from Biological aspect of Ancestor more info
involved_in calcium-ion regulated exocytosis	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in cerebellum development	IEP Inferred from Expression Pattern more info	PubMed
involved_in fat cell differentiation	IEA Inferred from Electronic Annotation more info
involved_in fat cell differentiation	ISO Inferred from Sequence Orthology more info
involved_in fat cell differentiation	ISS Inferred from Sequence or Structural Similarity more info
involved_in maintenance of synapse structure	ISO Inferred from Sequence Orthology more info
involved_in response to ethanol	IEP Inferred from Expression Pattern more info	PubMed
involved_in zymogen granule exocytosis	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
located_in Golgi apparatus	ISO Inferred from Sequence Orthology more info
located_in Golgi lumen	IEA Inferred from Electronic Annotation more info
located_in Golgi lumen	ISO Inferred from Sequence Orthology more info
located_in Golgi lumen	ISS Inferred from Sequence or Structural Similarity more info
located_in cytoplasm	IDA Inferred from Direct Assay more info	PubMed
is_active_in endoplasmic reticulum	IBA Inferred from Biological aspect of Ancestor more info
located_in late endosome	IDA Inferred from Direct Assay more info	PubMed
located_in late endosome	IEA Inferred from Electronic Annotation more info
located_in late endosome	ISO Inferred from Sequence Orthology more info
located_in late endosome	ISS Inferred from Sequence or Structural Similarity more info
located_in plasma membrane	IDA Inferred from Direct Assay more info	PubMed

General protein information

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Preferred Names: 45 kDa calcium-binding protein

Names: SDF-4; cab45

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_130412.2 → NP_569096.2 45 kDa calcium-binding protein

See identical proteins and their annotated locations for NP_569096.2

Status: PROVISIONAL

Source sequence(s)

BC086996

UniProtKB/Swiss-Prot

Q5PQW3, Q91ZS3

UniProtKB/TrEMBL

A0A8I6GL63, A6IUU8

Related

ENSRNOP00000095500.1, ENSRNOT00000106007.1

Conserved Domains (2) summary

pfam13499
Location:123 → 183

EF-hand_7; EF-hand domain pair

cl08302
Location:122 → 181

EFh; EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to ...

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_086023.1 Reference GRCr8

Range

171868591..171885827

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_063287106.1 → XP_063143176.1 45 kDa calcium-binding protein isoform X5
XM_063287105.1 → XP_063143175.1 45 kDa calcium-binding protein isoform X4
XM_039109194.2 → XP_038965122.1 45 kDa calcium-binding protein isoform X2

UniProtKB/Swiss-Prot

Q5PQW3, Q91ZS3

Conserved Domains (1) summary

cd16225
Location:87 → 383

EFh_CREC_cab45; EF-hand, calcium binding motif, found in 45 kDa calcium-binding protein (Cab45)
XM_039109193.2 → XP_038965121.1 45 kDa calcium-binding protein isoform X1

UniProtKB/Swiss-Prot

Q5PQW3, Q91ZS3

Conserved Domains (1) summary

cd16225
Location:94 → 390

EFh_CREC_cab45; EF-hand, calcium binding motif, found in 45 kDa calcium-binding protein (Cab45)
XM_006239516.5 → XP_006239578.1 45 kDa calcium-binding protein isoform X3

See identical proteins and their annotated locations for XP_006239578.1

UniProtKB/Swiss-Prot

Q5PQW3, Q91ZS3

UniProtKB/TrEMBL

A0A0G2JSR9, A6IUV0

Related

ENSRNOP00000027215.4

Conserved Domains (1) summary

cd16225
Location:94 → 374

EFh_CREC_cab45; EF-hand, calcium binding motif, found in 45 kDa calcium-binding protein (Cab45)