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SDF2L1 Gene

protein-coding   GIFtS: 52
GCID: GC22P021996

Stromal Cell-Derived Factor 2-Like 1

  Search for SDF2L1
at  

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
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Aliases
Stromal Cell-Derived Factor 2-Like 11 2     OTTHUMT000000750322
PWP1-Interacting Protein 81 2 3     SDF2-Like 12
Dihydropyrimidinase-Like 21 2     Stromal Cell-Derived Factor 2-Like Protein 12
SDF2-Like Protein 12 3     

External Ids:    HGNC: 106761   Entrez Gene: 237532   Ensembl: ENSG000001282287   OMIM: 6075515   UniProtKB: Q9HCN83   

Export aliases for SDF2L1 gene to outside databases

Previous GC identifers: GC22P018695 GC22P020320 GC22P020321 GC22P004954


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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GeneCards Summary for SDF2L1 Gene:
SDF2L1 (stromal cell-derived factor 2-like 1) is a protein-coding gene. An important paralog of this gene is SDF2.


(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 75), Regulatory elements and Epigenetics data according to QIAGEN, and/or SwitchGear Genomics)
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RefSeq DNA sequence at NCBI GenBank:
NC_000022.10  NC_018933.2  NT_011520.13  
Regulatory elements:
   Regulatory transcription factor binding sites in the SDF2L1 gene promoter:
         Pax-5   SREBP-1c   Brachyury   SREBP-1b   E47   YY1   GATA-1   MEF-2A   SREBP-1a   aMEF-2   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidSDF2L1 promoter sequence
   Search Chromatin IP Primers for SDF2L1

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat SDF2L1


Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: 22q11.21   Ensembl cytogenetic band:  22q11.21   HGNC cytogenetic band: 22q11.21

SDF2L1 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
SDF2L1 gene location

GeneLoc information about chromosome 22         GeneLoc Exon Structure

GeneLoc location for GC22P021996:  view genomic region     (about GC identifiers)

Start:
21,996,542 bp from pter      End:
21,998,588 bp from pter
Size:
2,047 bases      Orientation:
plus strand

(According to 1UniProtKB, HORDE, 2neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, Cloud-Clone Corp., and/or eBioscience,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, Cloud-Clone Corp., and/or eBioscience, Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, Cloud-Clone Corp, and/or others.)
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UniProtKB/Swiss-Prot: SDF2L_HUMAN, Q9HCN8 (See protein sequence)
Recommended Name: Stromal cell-derived factor 2-like protein 1 precursor  
Size: 221 amino acids; 23598 Da
Secondary accessions: A2RUD3 Q9BRI5

Explore the universe of human proteins at neXtProt for SDF2L1: NX_Q9HCN8

Explore proteomics data for SDF2L1 at MOPED

Post-translational modifications: 

  • Glycosylation2 at Ser211
  • Modification sites at PhosphoSitePlus

  • See SDF2L1 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins: NP_071327.2  
    ENSEMBL proteins: 
     ENSP00000248958  

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    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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    2 InterPro protein domains:
     IPR027005 GlyclTrfase_39_like
     IPR016093 MIR_motif

    Graphical View of Domain Structure for InterPro Entry Q9HCN8

    ProtoNet protein and cluster: Q9HCN8

    1 Blocks protein domain: IPB003608 MIR domain

    UniProtKB/Swiss-Prot: SDF2L_HUMAN, Q9HCN8
    Similarity: Contains 3 MIR domains


    Find genes that share domains with SDF2L1           About GenesLikeMe


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, inGenious Targeting Laboratory, genOway,
    transcription factor targeting from QIAGEN and/or HOMER, miRNA Gene Targets from miRTarBase, shRNA from OriGene, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, SwitchGear Genomics, Gene Editing from DNA2.0, Clones from OriGene, GenScript, Sino Biological, DNA2.0, Vector BioLabs and/or Addgene, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Flow cytometry from eBioscience, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Molecular Function:
         Genatlas biochemistry entry for SDF2L1:
    stromal cell-derived factor 2-like 1

    Phenotypes:
         2 GenomeRNAi human phenotypes for SDF2L1:
     Decreased TP53 protein express  Decreased homologous recombina 

    Animal Models:
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    miRTarBase miRNAs that target SDF2L1:
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    6 qRT-PCR Assays for microRNAs that regulate SDF2L1:
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    Browse SwitchGear 3'UTR luciferase reporter plasmids
    Inhib. RNA
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    (According to UniProtKB, COMPARTMENTS Subcellular localization database, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Subcellular locations from UniProtKB/Swiss-Prot
    SDF2L_HUMAN, Q9HCN8: Endoplasmic reticulum lumen (Potential)
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    endoplasmic reticulum3
    extracellular3

    Gene Ontology (GO): 2 cellular component terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005788endoplasmic reticulum lumen IEA--
    GO:0016020membrane IEA--

    Find genes that share ontologies with SDF2L1           About GenesLikeMe


    (SuperPaths according to PathCards, Pathways according to R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Sino Biological, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to QIAGEN, and/or STRING, Interactions according to 1UniProtKB, 2MINT, 3I2D, and/or 4STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene).
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        Custom Pathway & Disease-focused RT2 Profiler PCR Arrays for SDF2L1
    Interactions:

        Search GeneGlobe Interaction Network for SDF2L1

    STRING Interaction Network Preview (showing 5 interactants - click image to see 8)

    Selected Interacting proteins for SDF2L1 (Q9HCN83 ENSP000002489584) via UniProtKB, MINT, STRING, and/or I2D (see all 13)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    MYCP011063, ENSP000003672074I2D: score=1 STRING: ENSP00000367207
    UEVLDQ8IX043, ENSP000003795004I2D: score=1 STRING: ENSP00000379500
    RRP1BQ146843, ENSP000003391454I2D: score=1 STRING: ENSP00000339145
    TERF2Q155543, ENSP000002549424I2D: score=1 STRING: ENSP00000254942
    ATG5Q9H1Y03I2D: score=1 
    About this table

    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience, ApexBio, HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB)
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    Browse Small Molecules at EMD Millipore
       Browse drugs & compounds from Enzo Life Sciences
      Browse compounds at ApexBio 

    Browse Tocris compounds for SDF2L1 (SDF2L)



    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 236 Homo sapiens; Apr 25 2013) or GenBank,
    RefSeq according to Entrez Gene,
    DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
    exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN, SwitchGear Genomics,
    Tagged/untagged cDNA clones from OriGene, GenScript, DNA2.0, Vector BioLabs, and/or Addgene, Primers from OriGene, and/or QIAGEN, Flow cytometry from eBioscience )
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    REFSEQ mRNAs for SDF2L1 gene: 
    NM_022044.2  

    Unigene Cluster for SDF2L1:

    Stromal cell-derived factor 2-like 1
    Hs.303116  [show with all ESTs]
    Unigene Representative Sequence: BU588938
    2 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000248958(uc002zvf.3) ENST00000466935
    miRNA
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    hsa-miR-124 hsa-miR-1283 hsa-miR-186* hsa-miR-506 hsa-miR-543 hsa-miR-1224-5p
    Browse SwitchGear 3'UTR luciferase reporter plasmids
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      QuantiTect SYBR Green Assays in human, mouse, rat SDF2L1
      QuantiFast Probe-based Assays in human, mouse, rat SDF2L1

    Additional mRNA sequence: 

    AB043007.1 AF277316.1 AY359118.1 BC132849.1 BC132851.1 BC139837.1 CR456570.1 

    6 DOTS entries:

    DT.210345  DT.97782604  DT.100782168  DT.120651058  DT.40115176  DT.95347577 

    Selected AceView cDNA sequences (see all 144):

    BI858908 AF277316 BI826165 AI468402 BM048693 AW136812 AI638546 BG774895 
    AI739099 BU538689 CR456570 BI792867 AI985119 BE796310 BI793131 CA777258 
    BQ922787 BE388276 CA776971 BU956380 CR612706 BM312399 BG913385 AA383935 

    GeneLoc Exon Structure


    (RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MaxQB, plus additional links to SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from QIAGEN, Primers from OriGene, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
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    SDF2L1 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: GAAGGCATCT
    SDF2L1 Expression
    About this image


    SDF2L1 expression in embryonic tissues and stem cells    About this table
    Data from LifeMap, the Embryonic Development and Stem Cells Database
     selected tissues (see all 7) fully expand
     
     Brain (Nervous System)    fully expand to see all 3 entries
             Cerebral Cortex
     
     Trophoblast (Extraembryonic Tissues)
             Trophoblast Cells Trophoblast
     
     Ovary (Reproductive System)
             Oviduct
     
     Pancreas (Endocrine System)
             Islets of Langerhans
     
     Testis (Reproductive System)
             Leydig Cells Testis Interstitium
    SDF2L1 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    SDF2L1 Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.303116

    UniProtKB/Swiss-Prot: SDF2L_HUMAN, Q9HCN8
    Tissue specificity: Ubiquitously expressed with high expression in testis, moderate expression in the pancreas,
    spleen, prostate, small intestine and colon. Very low expression is seen in brain and skeletal muscle

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    In Situ
    Assay Products:
     

     
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    (Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD , 5MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or 6Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
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    This gene was present in the common ancestor of animals.

    Orthologs for SDF2L1 gene from Selected species (see all 15)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Sdf2l11 , 5 stromal cell-derived factor 2-like 11, 5 85.37(n)1
    89.14(a)1
      16 (10.62 cM)5
    641361  NM_022324.31  NP_071719.11 
     171301385 
    chicken
    (Gallus gallus)
    Aves SDF2L11 stromal cell-derived factor 2-like 1 72.25(n)
    82.7(a)
      416770  XM_001232857.3  XP_001232858.1 
    lizard
    (Anolis carolinensis)
    Reptilia SDF2L16
    stromal cell-derived factor 2-like 1
    71(a)
    1 ↔ 1
    GL343282.1(1175858-1180757)
    African clawed frog
    (Xenopus laevis)
    Amphibia Xl.54582 Xenopus laevis transcribed sequence with weak similarity more 72.22(n)    BJ042972.1 
    zebrafish
    (Danio rerio)
    Actinopterygii sdf2l11 stromal cell-derived factor 2-like 1 65.28(n)
    70.98(a)
      445275  NM_001003730.1  NP_001003730.2 
    fruit fly
    (Drosophila melanogaster)
    Insecta CG119993   -- 51(a)   82F10   --
    worm
    (Caenorhabditis elegans)
    Secernentea R12E2.133   -- 50(a)   I(4177363-4178553)   --


    ENSEMBL Gene Tree for SDF2L1 (if available)
    TreeFam Gene Tree for SDF2L1 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for SDF2L1 gene
    SDF22  
    1 SIMAP similar gene for SDF2L1 using alignment to 1 protein entry:     SDF2L_HUMAN:
    SDF2

    Find genes that share paralogs with SDF2L1           About GenesLikeMe



    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, 4UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD), the Human Cytochrome P450 Allele Nomenclature Database, and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers, Cancer Mutation PCR Arrays and Assays, and Copy Number PCR Arrays from QIAGEN)
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    Selected SNPs for SDF2L1 (see all 120)    About this table                                 

    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 22 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs1819844351,2
    --21994663(+) GAGATC/TGTGCC 1 -- us2k10--------
    rs2012221311,2
    --21994694(+) ACAGA-/GTAAGA 1 -- us2k10--------
    rs341131211,2
    C--21994737(+) AAAAAA/GGACTT 1 -- us2k10--------
    rs1859233091,2
    --21994898(+) ACATGG/TTGAAA 1 -- us2k10--------
    rs8618491,2
    C,F,A--21995031(-) gatctC/Tggctc 1 -- us2k13Minor allele frequency- T:0.27NA MN CSA 187
    rs1998203031,2
    C--21995086(+) AAAAA-/ATTGTT 1 -- us2k10--------
    rs1890707611,2
    --21995231(+) AGGGCA/GGAGAC 1 -- us2k10--------
    rs1386282181,2
    --21995314(+) CTCAGA/GTAGTA 1 -- us2k10--------
    rs1115603471,2
    C,F--21995531(+) TTCTGA/CACGCA 1 -- us2k12Minor allele frequency- C:0.10CSA WA 120
    rs1493202851,2
    C--21995633(+) ATTTGC/TTCTGT 1 -- us2k10--------

    HapMap Linkage Disequilibrium report for SDF2L1 (21996542 - 21998588 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 6 variations for SDF2L1:    About this table    
    Variant IDTypeSubtypePubMed ID
    dgv4882n71CNV Loss21882294
    nsv516806CNV Loss19592680
    nsv914458CNV Loss21882294
    nsv914469CNV Loss21882294
    dgv4881n71CNV Loss21882294
    nsv7350OTHER Inversion18451855

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    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
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    OMIM gene information: 607551    OMIM disorders: --


    Find genes that share disorders with SDF2L1           About GenesLikeMe

    Genetic Association Database (GAD): SDF2L1

    Export disorders for SDF2L1 gene to outside databases

    (in PubMed. Associations of this gene to articles via 1Entrez Gene, 2UniProtKB/Swiss-Prot, 3HGNC, 4GAD, 5PharmGKB, 6HMDB, 7DrugBank, 8UniProtKB/TrEMBL, 9 Novoseek, and/or 10fRNAdb)
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    PubMed articles for SDF2L1 gene, integrated from 10 sources (see all 17):
    (articles sorted by number of sources associating them with SDF2L1)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Murine and human SDF2L1 is an endoplasmic reticulum stress-inducible gene and encodes a new member of the Pmt/rt protein family. (PubMed id 11162531)1, 2, 3, 9 Fukuda S.... Kamiya K. (Biochem. Biophys. Res. Commun. 2001)
    2. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)1, 2 Gerhard D.S.... Malek J. (Genome Res. 2004)
    3. A genome annotation-driven approach to cloning the human ORFeome. (PubMed id 15461802)1, 2 Collins J.E.... Dunham I. (Genome Biol. 2004)
    4. The secreted protein discovery initiative (SPDI), a large-scale effort to identify novel human secreted and transmembrane proteins: a bioinformatics assessment. (PubMed id 12975309)1, 2 Clark H.F.... Gray A.M. (Genome Res. 2003)
    5. The DNA sequence of human chromosome 22. (PubMed id 10591208)1, 3 Dunham I.... Wright H. (Nature 1999)
    6. SDF2L1 interacts with the ER-associated degradation machinery and retards the degradation of mutant proinsulin in pancreatic I^-cells. (PubMed id 23444373)1 Tiwari A....Volchuk A. (J. Cell. Sci. 2013)
    7. Global landscape of HIV-human protein complexes. (PubMed id 22190034)1 JAoger S....Krogan N.J. (Nature 2012)
    8. A high-throughput approach for measuring temporal changes in the interactome. (PubMed id 22863883)1 Kristensen A.R....Foster L.J. (Nat. Methods 2012)
    9. Proteomic identification of common SCF ubiquitin ligase FBXO6-interacting glycoproteins in three kinds of cells. (PubMed id 22268729)1 Liu B....Wang L.S. (J. Proteome Res. 2012)
    10. Initial characterization of the human central proteome. (PubMed id 21269460)2 Burkard T.R.... Colinge J. (BMC Syst. Biol. 2011)

    (in PubMed, OMIM, and NCBI Bookshelf)
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      Query String
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    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
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    Entrez Gene: 23753 HGNC: 10676 AceView: SDF2L1 Ensembl:ENSG00000128228 euGenes: HUgn23753
    ECgene: SDF2L1 H-InvDB: SDF2L1

    (According to HUGE)
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      --

    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, and/or others, e.g. Wikipedia and GeneReviews, via UniProtKB/Swiss-Prot)
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    NameDescription
    PharmGKB entry for SDF2L1 Pharmacogenomics, SNPs, Pathways
    ATLAS Chromosomes in Cancer entry for SDF2L1 Genetics and Cytogenetics in Oncology and Haematology

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
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    Patent Information for SDF2L1 gene:
    Search GeneIP for patents involving SDF2L1

    GeneCards and IP:
    Japan Patent Office Licenses GeneCards     European Patent Office Licenses GeneCards     Improving the IP Search



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