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SDF2 stromal cell derived factor 2 [ Homo sapiens (human) ]

Gene ID: 6388, updated on 5-Mar-2024

Summary

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Official Symbol
SDF2provided by HGNC
Official Full Name
stromal cell derived factor 2provided by HGNC
Primary source
HGNC:HGNC:10675
See related
Ensembl:ENSG00000132581 MIM:602934; AllianceGenome:HGNC:10675
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
Summary
The protein encoded by this gene is believed to be a secretory protein. It has regions of similarity to hydrophilic segments of yeast mannosyltransferases. Its expression is ubiquitous and the gene appears to be relatively conserved among mammals. Alternate splicing results in both coding and non-coding variants. A pseudogene of this gene is located on chromosome 15. [provided by RefSeq, Dec 2011]
Expression
Ubiquitous expression in adrenal (RPKM 19.5), placenta (RPKM 16.0) and 25 other tissues See more
Orthologs
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Genomic context

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See SDF2 in Genome Data Viewer
Location:
17q11.2
Exon count:
5
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 17 NC_000017.11 (28648346..28662194, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (29591070..29604958, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 17 NC_000017.10 (26975364..26989212, complement)

Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene SPAG5 antisense RNA 1 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr17:26938368-26939567 Neighboring gene ribosomal protein S6 kinase related Neighboring gene bridge-like lipid transfer protein family member 2 Neighboring gene ReSE screen-validated silencer GRCh37_chr17:26954912-26955086 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8346 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8347 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr17:26988611-26989810 Neighboring gene ribosomal protein S12 pseudogene 28 Neighboring gene SPT6 homolog, histone chaperone and transcription elongation factor Neighboring gene Sharpr-MPRA regulatory region 10516 Neighboring gene H3K27ac-H3K4me1 hESC enhancers GRCh37_chr17:27037571-27038346 and GRCh37_chr17:27038347-27039122 Neighboring gene protein interacting with cyclin A1

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • 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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Related articles in PubMed

  1. Stromal Cell-Derived Factor (SDF) 2 and the Endoplasmic Reticulum Stress Response of Trophoblast Cells in Gestational Diabetes Mellitus and In vitro Hyperglycaemic Condition. Lorenzon AR, et al. Curr Vasc Pharmacol, 2021. PMID 32504504
  2. Stromal Cell-Derived Factor 2: A Novel Protein that Interferes in Endoplasmic Reticulum Stress Pathway in Human Placental Cells. Lorenzon-Ojea AR, et al. Biol Reprod, 2016 Aug. PMID 27335075, Free PMC Article
  3. Protection of stromal cell-derived factor 2 by heat shock protein 72 prevents oxaliplatin-induced cell death in oxaliplatin-resistant human gastric cancer cells. Takahashi K, et al. Cancer Lett, 2016 Aug 1. PMID 27157913
  4. Stromal cell-derived factor 2 is critical for Hsp90-dependent eNOS activation. Siragusa M, et al. Sci Signal, 2015 Aug 18. PMID 26286023, Free PMC Article
  5. Isolation and characterization of a novel secretory protein, stromal cell-derived factor-2 (SDF-2) using the signal sequence trap method. Hamada T, et al. Gene, 1996 Oct 17. PMID 8918255

See all (49) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Stromal Cell-Derived Factor (SDF) 2 and the Endoplasmic Reticulum Stress Response of Trophoblast Cells in Gestational Diabetes Mellitus and In vitro Hyperglycaemic Condition.
    Title: Stromal Cell-Derived Factor (SDF) 2 and the Endoplasmic Reticulum Stress Response of Trophoblast Cells in Gestational Diabetes Mellitus and In vitro Hyperglycaemic Condition.
  2. SDF2 associates with ERdj3 and acts as a component in the BiP chaperone cycle to prevent the aggregation of misfolded proteins.
    Title: Endoplasmic reticulum proteins SDF2 and SDF2L1 act as components of the BiP chaperone cycle to prevent protein aggregation.
  3. These findings suggest that SDF2 may be an important regulatory factor by which trophoblast cells can control cell survival under ER stress.
    Title: Stromal Cell-Derived Factor 2: A Novel Protein that Interferes in Endoplasmic Reticulum Stress Pathway in Human Placental Cells.
  4. Hsp72 prevented SDF-2 degradation in a chaperone activity-dependent manner avoiding oxaliplatin-induced cell death in oxaliplatin-resistant human gastric cancer cells.
    Title: Protection of stromal cell-derived factor 2 by heat shock protein 72 prevents oxaliplatin-induced cell death in oxaliplatin-resistant human gastric cancer cells.
  5. Data indicate a function for stromal cell-derived factor 2 (SDF2) as a component of the heat-shock proteins 90-endothelial nitric oxide synthase (Hsp90-eNOS) complex that is critical for signal transduction in endothelial cells.
    Title: Stromal cell-derived factor 2 is critical for Hsp90-dependent eNOS activation.
  6. SDF-2, SDF-4 and SDF-5 are expressed in mammary tissues and cells and that a reduced level of SDF-2 and SDF-4 are associated with a poor clinical outcome.
    Title: Transcript analyses of stromal cell derived factors (SDFs): SDF-2, SDF-4 and SDF-5 reveal a different pattern of expression and prognostic association in human breast cancer.
  7. Observational study of gene-disease association. (HuGE Navigator)
    Title: Phenotype-genotype interactions on renal function in type 2 diabetes: an analysis using structural equation modelling.
Submit: New GeneRIF Correction

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

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)

Genotypes

HIV-1 interactions

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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 2 (SDF2) in human HEK293 and/or Jurkat cell lines by using affinity tagging and purification mass spectrometry analyses PubMed
Envelope surface glycoprotein gp160, precursor env HIV-1 gp160 is identified to have a physical interaction with stromal cell-derived factor 2 (SDF2) 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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Markers

Homology

Clone Names

  • FLJ17932

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables misfolded protein binding IMP
Inferred from Mutant Phenotype
more info
 PubMed 
Process Evidence Code Pubs
involved_in chaperone cofactor-dependent protein refolding IMP
Inferred from Mutant Phenotype
more info
 PubMed 
Component Evidence Code Pubs
located_in endoplasmic reticulum IDA
Inferred from Direct Assay
more info
 PubMed 
part_of protein folding chaperone complex IPI
Inferred from Physical Interaction
more info
 PubMed 

General protein information

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Preferred Names
stromal cell-derived factor 2
Names
SDF-2

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)

  1. NM_006923.4 → NP_008854.2  stromal cell-derived factor 2 precursor

    See identical proteins and their annotated locations for NP_008854.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longer transcript and encodes the functional protein.
    Source sequence(s)
    AC005726, AW026433, BC001406, BQ056236
    Consensus CDS
    CCDS11238.1
    UniProtKB/Swiss-Prot
    Q99470, Q9BQ79
    UniProtKB/TrEMBL
    Q6IBU4
    Related
    ENSP00000247020.3, ENST00000247020.9
    Conserved Domains (1) summary
    COG1928
    Location:14 → 188
    PMT1; Dolichyl-phosphate-mannose--protein O-mannosyl transferase [Posttranslational modification, protein turnover, chaperones]

RNA

  1. NR_045585.2 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) contains an alternate 5' exon, compared to variant 1. This variant is represented as non-coding because it lacks a large portion of the coding region, including the translational start codon, found in variant 1.
    Source sequence(s)
    AC005726, AC010761, AW026433, BC001406, CD673481
    Related
    ENST00000592250.5

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000017.11 Reference GRCh38.p14 Primary Assembly

    Range
    28648346..28662194 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047436516.1 → XP_047292472.1  stromal cell-derived factor 2 isoform X2

    UniProtKB/Swiss-Prot
    Q99470, Q9BQ79
    UniProtKB/TrEMBL
    Q6IBU4

  2. XM_011525106.3 → XP_011523408.1  stromal cell-derived factor 2 isoform X1

    See identical proteins and their annotated locations for XP_011523408.1

    Conserved Domains (1) summary
    smart00472
    Location:83 → 157
    MIR; Domain in ryanodine and inositol trisphosphate receptors and protein O-mannosyltransferases

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060941.1 Alternate T2T-CHM13v2.0

    Range
    29591070..29604958 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054316877.1 → XP_054172852.1  stromal cell-derived factor 2 isoform X2

    UniProtKB/Swiss-Prot
    Q99470, Q9BQ79
    UniProtKB/TrEMBL
    Q6IBU4

  2. XM_054316876.1 → XP_054172851.1  stromal cell-derived factor 2 isoform X1

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q99470.2 GenPept UniProtKB/Swiss-Prot:Q99470

Gene LinkOut

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