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

    Gene ID: 6388, updated on 2-Nov-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
    mouse all
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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_2024_08 current GRCh38.p14 (GCF_000001405.40) 17 NC_000017.11 (28648346..28662194, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (29591070..29604958, complement)
    RS_2024_09 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 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 2 is critical for Hsp90-dependent eNOS activation. Siragusa M, et al. Sci Signal, 2015 Aug 18. PMID 26286023, Free PMC Article
    2. 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
    3. 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
    4. 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
    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 (53) 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_2024_08

    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

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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