SDF4 stromal cell derived factor 4 [Homo sapiens (human)] - Gene

Summary

Official Symbol: SDF4provided by HGNC
Official Full Name: stromal cell derived factor 4provided by HGNC
Primary source: HGNC:HGNC:24188
See related: Ensembl:ENSG00000078808 MIM:614282; AllianceGenome:HGNC:24188
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: Cab45; SDF-4
Summary: This gene encodes a stromal cell derived factor that is a member of the CREC protein family. The encoded protein contains six EF-hand motifs and calcium-binding motifs. This protein localizes to the Golgi lumen and may be involved in regulating calcium dependent cellular activities. [provided by RefSeq, Sep 2011]
Expression: Ubiquitous expression in colon (RPKM 31.3), kidney (RPKM 26.5) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 1p36.33

Exon count:: 8

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	1	NC_000001.11 (1216931..1232001, complement)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	1	NC_060925.1 (645388..660462, complement)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	1	NC_000001.10 (1152311..1167381, complement)

Chromosome 1 - NC_000001.11 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
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?

LINC00173 facilitates tumor progression by stimulating RAB1B-mediated PA2G4 and SDF4 secretion in nasopharyngeal carcinoma.
Title: LINC00173 facilitates tumor progression by stimulating RAB1B-mediated PA2G4 and SDF4 secretion in nasopharyngeal carcinoma.
Cab45 deficiency leads to the mistargeting of progranulin and prosaposin and aberrant lysosomal positioning.
Title: Cab45 deficiency leads to the mistargeting of progranulin and prosaposin and aberrant lysosomal positioning.
SDF4 Is a Prognostic Factor for 28-Days Mortality in Patients With Sepsis via Negatively Regulating ER Stress.
Title: SDF4 Is a Prognostic Factor for 28-Days Mortality in Patients With Sepsis via Negatively Regulating ER Stress.
Fam20C regulates protein secretion by Cab45 phosphorylation.
Title: Fam20C regulates protein secretion by Cab45 phosphorylation.
Ca(2+)-dependent changes in Cab45 mediate sorting of specific cargo molecules at the trans-Golgi network.
Title: Secretory cargo sorting by Ca2+-dependent Cab45 oligomerization at the trans-Golgi network.
Data reveal that the ability of Cab45S to inhibit SERCA2b activity is crucial for its role as a modulator of cell proliferation and tumor growth.
Title: Cab45S promotes cell proliferation through SERCA2b inhibition and Ca2+ signaling.
The obtained results indicate that the changes in gene expression in bone marrow progenitor cells can be involved into space flight-induced osteopenia.
Title: [The effects of simulated microgravity on the pattern of gene expression in human bone marrow mesenchymal stem cells under osteogenic differentiation].
Cab45S, a novel regulator of GRP78/BiP, suppresses endoplasmic reticulum stress-induced IRE1 activation and apoptosis by binding to and elevating GRP78/BiP, and has a role in the inhibition of ER stress-induced apoptosis.
Title: Cab45S inhibits the ER stress-induced IRE1-JNK pathway and apoptosis via GRP78/BiP.
Calcium is required for the retention of Cab45 in the Golgi membranes, where Cab45 binds secretory cargo in a calcium-dependent reaction.
Title: Cab45 is required for Ca(2+)-dependent secretory cargo sorting at the trans-Golgi network.
Observational study of gene-disease association, gene-environment interaction, and pharmacogenomic / toxicogenomic. (HuGE Navigator)
Title: Variation at the NFATC2 locus increases the risk of thiazolidinedione-induced edema in the Diabetes REduction Assessment with ramipril and rosiglitazone Medication (DREAM) study.

Submit: New GeneRIF Correction See all GeneRIFs (13)

Phenotypes

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Review eQTL and phenotype association data in this region using PheGenI

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

HIV-1 interactions

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Replication interactions

Interaction	Pubs
Knockdown of stromal cell derived factor 4 (SDF4) by siRNA inhibits the early stages of HIV-1 replication in 293T cells infected with VSV-G pseudotyped HIV-1	PubMed

Protein interactions

Protein	Gene	Interaction	Pubs
Envelope surface glycoprotein gp120	env	HIV-1 gp120 is identified to have a physical interaction with stromal cell derived factor 4 (SDF4) in human HEK293 and/or Jurkat cell lines by using affinity tagging and purification mass spectrometry analyses	PubMed

Go to the HIV-1, Human Interaction Database

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables calcium ion binding	IBA Inferred from Biological aspect of Ancestor more info
enables calcium ion binding	IDA Inferred from Direct Assay more info	PubMed
enables calcium ion binding	ISS Inferred from Sequence or Structural Similarity more info
enables identical protein binding	ISS Inferred from Sequence or Structural Similarity more info	PubMed
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in UV protection	ISS Inferred from Sequence or Structural Similarity more info	PubMed
involved_in calcium-ion regulated exocytosis	IBA Inferred from Biological aspect of Ancestor more info
involved_in calcium-ion regulated exocytosis	ISS Inferred from Sequence or Structural Similarity more info	PubMed
involved_in cerebellum development	ISS Inferred from Sequence or Structural Similarity more info	PubMed
involved_in fat cell differentiation	ISS Inferred from Sequence or Structural Similarity more info
involved_in maintenance of synapse structure	IGI Inferred from Genetic Interaction more info	PubMed
involved_in response to ethanol	ISS Inferred from Sequence or Structural Similarity more info	PubMed
involved_in zymogen granule exocytosis	ISS Inferred from Sequence or Structural Similarity more info	PubMed

Component	Evidence Code	Pubs
located_in Golgi lumen	ISS Inferred from Sequence or Structural Similarity more info
located_in bleb	IEA Inferred from Electronic Annotation more info
located_in cytoplasm	ISS Inferred from Sequence or Structural Similarity more info	PubMed
is_active_in endoplasmic reticulum	IBA Inferred from Biological aspect of Ancestor more info
located_in extracellular exosome	HDA more info	PubMed
located_in late endosome	ISS Inferred from Sequence or Structural Similarity more info
located_in membrane	HDA more info	PubMed
colocalizes_with plasma membrane	ISS Inferred from Sequence or Structural Similarity more info	PubMed

General protein information

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Preferred Names: 45 kDa calcium-binding protein

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.

Genomic

NG_030007.1 RefSeqGene

Range

5067..20137

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_016176.6 → NP_057260.3 45 kDa calcium-binding protein isoform 2 precursor

Status: REVIEWED

Description

Transcript Variant: This variant (2) uses a different splice site in the 3' coding region, compared to variant 1, that results in a frameshift. It encodes isoform 2, which has a shorter and distinct C-terminus compared to isoform 1.

Source sequence(s)

AL162741

Consensus CDS

CCDS30553.2

UniProtKB/TrEMBL

A0A5F9UP49

Related

ENSP00000353094.7, ENST00000360001.12

Conserved Domains (1) summary

cd16225
Location:60 → 340

EFh_CREC_cab45; EF-hand, calcium binding motif, found in 45 kDa calcium-binding protein (Cab45)
NM_016547.3 → NP_057631.2 45 kDa calcium-binding protein isoform 1 precursor

Status: REVIEWED

Description

Transcript Variant: This variant (1) represents the longer transcript yet it encodes the shorter protein (isoform 1).

Source sequence(s)

AF178986, AL162741, R15491

Consensus CDS

CCDS12.2

UniProtKB/TrEMBL

A0A5F9UJX7

Related

ENSP00000263741.8, ENST00000263741.12

Conserved Domains (1) summary

cd16225
Location:60 → 297

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

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000001.11 Reference GRCh38.p14 Primary Assembly

Range

1216931..1232001 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_047422111.1 → XP_047278067.1 45 kDa calcium-binding protein isoform X1

UniProtKB/Swiss-Prot

B1AME5, B1AME6, B2RDF1, B4DSM1, Q53G52, Q53HQ9, Q8NBQ3, Q96AA1, Q9BRK5, Q9NZP7, Q9UN53
XM_047422112.1 → XP_047278068.1 45 kDa calcium-binding protein isoform X2
XM_011541556.2 → XP_011539858.1 45 kDa calcium-binding protein isoform X3

See identical proteins and their annotated locations for XP_011539858.1

UniProtKB/Swiss-Prot

Q9BRK5

Conserved Domains (2) summary

cd00051
Location:102 → 161

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 ...

pfam13499
Location:103 → 163

EF-hand_7; EF-hand domain pair