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Category   Symbol Source: HGNC EntrezGene Ensembl GeneCards RNA genes CroW21
GIFtS

KHDRBS2 Gene

protein-coding   GIFtS: 49
GCID: GC06M062447

KH domain containing, RNA binding, signal transduction associated...

 Explore 2 diseases affiliated with
KHDRBS2 via our new
 Human Malady Compendium 
Biological research products
for KHDRBS2
    

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, and/or 10fRNAdb)
About This Section

Aliases
KH Domain Containing, RNA Binding, Signal Transduction Associated 21 2     Sam68-Like Mammalian Protein 12 3
SLM-11 2 3     MGC266641
SLM11 2 3     BA535F17.11
HSLM-11     KH Domain-Containing, RNA-Binding, Signal Transduction-Associated Protein 22

External Ids:    HGNC: 181141   Entrez Gene: 2025592   Ensembl: ENSG000001122327   OMIM: 6104875   UniProtKB: Q5VWX13   

Export aliases for KHDRBS2 gene to outside databases

Previous GC identifers: GC00U991173 GC06M062386 GC06M059556


(According to Entrez Gene, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
About This Section

UniProtKB/Swiss-Prot: KHDR2_HUMAN, Q5VWX1
Function: RNA-binding protein that plays a role in the regulation of alternative splicing and influences mRNA splice
site selection and exon inclusion. Its phosphorylation by FYN inhibits its ability to regulate splice site selection.
Induces an increased concentration-dependent incorporation of exon in CD44 pre-mRNA by direct binding to purine-rich
exonic enhancer. May function as an adapter protein for Src kinases during mitosis. Binds both poly(A) and poly(U)
homopolymers. Phosphorylation by PTK6 inhibits its RNA-binding ability (By similarity)




(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 69), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section
RefSeq DNA sequence:
NC_000006.11  NC_018917.1  NT_007299.13  
Regulatory elements:
   SABiosciences Regulatory transcription factor binding sites in the KHDRBS2 gene promoter:
         TBP   Nkx2-2   RORalpha2   Evi-1   SRY   Nkx6-1   HFH-1   NF-Y   RSRFC4   CBF(2)   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidKHDRBS2 promoter sequence
   Search SABiosciences Chromatin IP Primers for KHDRBS2

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat KHDRBS2


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

Entrez Gene cytogenetic band: 6q11.1   Ensembl cytogenetic band:  6q11.1   HGNC chromosome: 6

KHDRBS2 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
KHDRBS2 gene location

GeneLoc information about chromosome 6         GeneLoc Exon Structure

GeneLoc location for GC06M062447:  view genomic region     (about GC identifiers)

Start:
62,389,865 bp from pter      End:
62,996,132 bp from pter
Size:
606,268 bases      Orientation:
minus strand

(According to 1UniProtKB, HORDE, neXtProt, Ensembl, and/or Reactome, Modification sites according to 2PhosphoSitePlus, Specific Peptides from DME, Protein expression images according to data from SPIRE MOPED and PaxDb, 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, and/or Uscn,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Uscn, Ontologies according to Gene Ontology Consortium 01 Mar 2013 and Entrez Gene, Antibodies by EMD Millipore, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, Abcam, and/or Uscn)
About This Section

UniProtKB/Swiss-Prot: KHDR2_HUMAN, Q5VWX1 (See protein sequence)
Recommended Name: KH domain-containing, RNA-binding, signal transduction-associated protein 2  
Size: 349 amino acids; 38927 Da
Subunit: Self-associates to form homooligomers. Interacts with SAFB, SFRS9 and YTHDC1. Found in a complex with KHDRBS1,
KHDRBS2 and KHDRBS3. Interacts with the SH3 domains of FYN and PLCG1. Interacts with the SH2 domains of FYN, GRAP2,
PLCG1 and RASA1 (By similarity). Interacts with RBMX
Subcellular location: Nucleus (By similarity)
Secondary accessions: A8K7M8 Q8N4I4 Q8TCZ4

Explore the universe of human proteins at neXtProt for KHDRBS2: NX_Q5VWX1

Post-translational modifications:

  • Methylated1
  • Tyrosine phosphorylated by FYN, PTK6 and SRC. Tyrosine phosphorylated by SRC during mitosis (By similarity)1
  • View modification sites using PhosphoSitePlus2
  • View neXtProt modification sites for NX_Q5VWX1

  • KHDRBS2 Protein expression data from MOPED and PaxDb:    About this image 
    Estimated protein expression log10 (pmol).

    REFSEQ proteins: NP_689901.2  
    ENSEMBL proteins: 
     ENSP00000281156  

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    Uscn Proteins for KHDRBS2

    Gene Ontology (GO): 1 cellular component term (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005634nucleus IEA--


    KHDRBS2 for ontologies           About GeneDecksing



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    (According to InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
    About This Section

    KHDRBS2 for domains           About GeneDecksing

    2 InterPro domains/families:
     IPR004087 KH_dom
     IPR004088 KH_dom_type_1

    Graphical View of Domain Structure for InterPro Entry Q5VWX1

    ProtoNet protein and cluster: Q5VWX1

    1 Blocks protein family: IPB004087 KH domain

    UniProtKB/Swiss-Prot: KHDR2_HUMAN, Q5VWX1
    Similarity: Belongs to the KHDRBS family
    Similarity: Contains 1 KH domain


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013,
    bound targets from SABiosciences, miRNA Gene Targets from miRTarBase shRNA from OriGene, RNAi from EMD Millipore, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, Gene Editing from DNA2.0, Clones from EMD Millipore, OriGene, SwitchGear Genomics, GenScript, Sino Biological, DNA2.0, and Vector BioLabs, Cell Lines from GenScript, LifeMap BioReagents, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Mar 2013 via Entrez Gene.)
    About This Section

    Function Summary:

         UniProtKB/Swiss-Prot: KHDR2_HUMAN, Q5VWX1
    Function: RNA-binding protein that plays a role in the regulation of alternative splicing and influences mRNA splice
    site selection and exon inclusion. Its phosphorylation by FYN inhibits its ability to regulate splice site selection.
    Induces an increased concentration-dependent incorporation of exon in CD44 pre-mRNA by direct binding to purine-rich
    exonic enhancer. May function as an adapter protein for Src kinases during mitosis. Binds both poly(A) and poly(U)
    homopolymers. Phosphorylation by PTK6 inhibits its RNA-binding ability (By similarity)

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    hsa-miR-323-3p hsa-miR-579 hsa-miR-3685 hsa-miR-200a hsa-miR-570 hsa-miR-374c hsa-miR-141 hsa-miR-889
    SwitchGear 3'UTR luciferase reporter plasmidKHDRBS2 3' UTR sequence
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    Gene Ontology (GO): 5/6 molecular function terms (GO ID links to tree view) (see all 6):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005515protein binding IPI16189514
    GO:0008143poly(A) RNA binding IEA--
    GO:0008266poly(U) RNA binding IEA--
    GO:0017124SH3 domain binding IEA--
    GO:0042169SH2 domain binding IEA--


    KHDRBS2 for ontologies           About GeneDecksing



    (Pathways according to EMD Millipore, R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to SABiosciences, 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 Mar 2013 via Entrez Gene).
    About This Section



    Interactions:

        Search SABiosciences Gene Network CentralTM Interacting Genes and Proteins Networks for KHDRBS2

    STRING Interaction Network Preview (showing 5 interactants - click image to see 25)

    5/64 Interacting proteins for KHDRBS2 (Q5VWX11, 2, 3 ENSP000002811564) via UniProtKB, MINT, STRING, and/or I2D (see all 64)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    KHDRBS3O755252, 3, ENSP000003481084MINT-67800 I2D: score=4 STRING: ENSP00000348108
    RBMXP381591, 3, ENSP000003596454EBI-742808,EBI-743526 I2D: score=4 STRING: ENSP00000359645
    ARID2Q68CP93, ENSP000003350444I2D: score=1 STRING: ENSP00000335044
    DDX5P178443, ENSP000002257924I2D: score=1 STRING: ENSP00000225792
    DSG1Q024133, ENSP000002571924I2D: score=1 STRING: ENSP00000257192
    About this table

    Gene Ontology (GO): 2 biological process terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0006351transcription, DNA-dependent IEA--
    GO:0006355regulation of transcription, DNA-dependent IEA--


    KHDRBS2 for ontologies           About GeneDecksing



    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience HMDB, BitterDB, and/or Novoseek, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB, with drugs/clinical trials/news search links to CenterWatch)
    About This Section

    KHDRBS2 for compounds           About GeneDecksing

    Browse Small Molecules at EMD Millipore
    Browse drugs & compounds from Enzo Life Sciences

    Browse Tocris compounds for KHDRBS2
    1 Novoseek chemical compound relationship for KHDRBS2 gene    About this table
    Compound   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
    tyrosine 21.6 1 10077576 (1)

    Search CenterWatch for drugs/clinical trials and news about KHDRBS2 / KHDR2 

    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 235 Homo sapiens; Mar 10 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,
    RNAi Products from EMD Millipore,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN,
    Tagged/untagged cDNA clones from OriGene, SwitchGear Genomics, GenScript, DNA2.0, Vector BioLabs, Primers from OriGene, SABiosciences, and/or QIAGEN )
    About This Section

    REFSEQ mRNAs for KHDRBS2 gene: 
    NM_152688.2  

    Unigene Cluster for KHDRBS2:

    KH domain containing, RNA binding, signal transduction associated 2
    Hs.519794  [show with all ESTs]
    Unigene Representative Sequence: BC034043
    1 Ensembl transcript including schematic representation, and UCSC links where relevant:
    ENST00000281156(uc003peg.2)

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    hsa-miR-323-3p hsa-miR-579 hsa-miR-3685 hsa-miR-200a hsa-miR-570 hsa-miR-374c hsa-miR-141 hsa-miR-889
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      QIAGEN QuantiTect SYBR Green Assays in human, mouse, rat KHDRBS2
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    Additional cDNA sequence: 

    AK095983.1 AK292043.1 AY077838.1 BC034043.1 

    5 DOTS entries:

    DT.86850461  DT.97789343  DT.70101114  DT.91804988  DT.40207375 

    17 AceView cDNA sequences:

    AY077838 BC034043 AI632331 BG706672 AK095983 NM_152688 AW003449 BM926834 
    BP348510 BG195963 BM545404 AA385275 BI597067 D60325 R20052 CB987746 
    BM926281 

    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™, plus additional links to Genevestigator, and/or SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from SABiosciences, Primers from OriGene, SABiosciences, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
    About This Section

    KHDRBS2 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS
    CGAP TAG: TTAATGGAAA

    Microarray
    RNAseq (Illumina Body Map)
    (100×FPKM)½
    SAGE (Serial Analysis of Gene Expression)

    About this image

    KHDRBS2 expression in embryonic tissues and stem cells
    Expression by the Database of Embryonic development, Stem cell research, and Regenerative medicine    About this table
    1 LifeMap In Vivo Development Anatomical Compartment/Cell 
    Tissue Anatomical Compartment CellCategory (developmental path)
    BrainBlood Brain BarrierEndothelial CellsBlood Brain Barrier, Endothelium
    Expression: Positive    Negative     Selective marker
    Experimental details: Curated     Microarrays     In-situ hybridization
    Stem Cell Differentiation: 1 LifeMap Cell 
    NameCategory
    Line H9 (WA09) (Embryonic Stem Cell)Early Embryo, Inner Cell Mass

    See KHDRBS2 Protein Expression from SPIRE MOPED and PaxDB
    Genevestigator expression for KHDRBS2

    SOURCE GeneReport for Unigene cluster: Hs.519794

    UniProtKB/Swiss-Prot: KHDR2_HUMAN, Q5VWX1
    Tissue specificity: Highly expressed in brain, lung, kidney and small intestine. Weakly expressed in placenta, liver,
    spleen, thymus, ovary and colon

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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)
    About This Section

    This gene was present in the common ancestor of eukaryotes.

    Orthologs for KHDRBS2 gene from 5/20 species (see all 20)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    chicken
    (Gallus gallus)
    Aves KHDRBS21 KH domain containing, RNA binding, signal transduction more 84.87(n)
    92.82(a)
      428643  XM_426201.3  XP_426201.2 
    zebrafish
    (Danio rerio)
    Actinopterygii khdrbs21 KH domain containing, RNA binding, signal transduction more 70.92(n)
    74.2(a)
      768147  NM_001077290.1  NP_001070758.1 
    fruit fly
    (Drosophila melanogaster)
    Insecta CG39276
    CG40216
    (see all 8)
    --
    33(a)
    29(a)
    (see all 8)
    many ↔ many
    many ↔ many
    (see all 8)
    2R(18482193-18483858)
    2R(17660852-17662381)
    thale cress
    (Arabidopsis thaliana)
    eudicotyledons AT2G386106
    AT3G086206
    (see all 5)
    RNA-binding KH domain-containing protein
    (see all 5)
    27(a)
    26(a)
    (see all 5)
    many ↔ many
    many ↔ many
    (see all 5)
    2(16147113-16149873)
    3(2617768-2620573)
    rice
    (Oryza sativa)
    Liliopsida --
    --
    (see all 7)
    KH domain containing protein, putative, expressed
    (see all 7)
    27(a)
    27(a)
    (see all 7)
    many ↔ many
    many ↔ many
    (see all 7)
    5(23610169-23614751)
    3(34179264-34183709)


    ENSEMBL Gene Tree for KHDRBS2 (if available)
    TreeFam Gene Tree for KHDRBS2 (if available) 

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
    About This Section
    Paralogs for KHDRBS2 gene
    SF12  KHDRBS32  KHDRBS12  QKI2  
    3 SIMAP similar genes for KHDRBS2 using alignment to 2 protein entries:     KHDR2_HUMAN (see all proteins):
    KHDRBS3    KHDRBS1    QKI

    KHDRBS2 for paralogs           About GeneDecksing



    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, UniProtKB, 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) and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers from QIAGEN, Cancer Mutation PCR Arrays and Assays and Copy Number PCR Arrays from SABiosciences)
    About This Section

    10/10266 NCBI SNPs in KHDRBS2 are shown (see all 10266    About this table
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 6 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs709931941,2
    C--59902685(+) TATTA-/TTTTTTTT 1 -- int11Minor allele frequency- TTT:0.00NA 2
    rs117532211,2
    H--62389392(+) GAGTTA/TCTATT 1 -- int14Minor allele frequency- T:0.00NS EA 420
    rs1162403721,2
    --62389402(+) TAGTGT/CTACCT 1 -- int11Minor allele frequency- C:0.01NA 120
    rs1471004501,2
    --62389552(+) AATAAA/CGTTTT 1 -- int10--------
    rs1903190481,2
    --62389716(+) TGTGCA/GGGGAA 1 -- int10--------
    rs1810821821,2
    --62389736(+) TTGAAA/GAACTA 1 -- int10--------
    rs1481278311,2
    --62389793(+) TTACTC/GTTTCT 1 -- int10--------
    rs1411032481,2
    --62389829(+) AGTCAA/GTCAGA 1 -- int10--------
    rs1857317211,2
    --62389879(+) AATCCA/TTTTAT 1 -- ut310--------
    rs1898012311,2
    --62390046(+) GGGTTA/CATTTT 1 -- ut310--------

    HapMap Linkage Disequilibrium report for KHDRBS2 (62389865 - 62639865 bp, first 250kb of KHDRBS2)
    Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions)
    Database of Genomic Variants (DGV): 9 variations for KHDRBS2
         7 CNVs: 39453 53197 7580 51935 64529 0081 38645
         2 Indels: 28344 47146

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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.)
    About This Section

    KHDRBS2 for disorders           About GeneDecksing

    OMIM gene information: 610487    OMIM disorders: --

    2 diseases for KHDRBS2:    About MalaCards
    immunodeficiency    malaria


    Export disorders for KHDRBS2 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)
    About This Section

    PubMed articles for KHDRBS2 gene, integrated from 9 sources (see all 22):
    (articles sorted by number of sources associating them with KHDRBS2)
        Utopia: connect your pdf to the dynamic
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    1. Cloning and characterization of a novel human STAR domain containing cDNA KHDRBS2. (PubMed id 12549823)1, 2, 9 Wang L.... Mao Y. (2002)
    2. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1, 2 Ota T.... Sugano S. (2004)
    3. Sam68 RNA binding protein is an in vivo substrate for protein arginine N-methyltransferase 1. (PubMed id 12529443)1, 2 Cote J.... Richard S. (2003)
    4. Characterization of Sam68-like mammalian proteins SLM-1 and SLM-2: SLM-1 is a Src substrate during mitosis. (PubMed id 10077576)1, 9 Di Fruscio M.... Richard S. (1999)
    5. Methods for quantification of in vivo changes in prote in ubiquitination following proteasome and deubiquitinase inhibition. (PubMed id 22505724)1 Udeshi N.D....Carr S.A. (2012)
    6. Functional dissection of lysine deacetylases reveals t hat HDAC1 and p300 regulate AMPK. (PubMed id 22318606)1 Lin Y.Y....Boeke J.D. (2012)
    7. Systematic and quantitative assessment of the ubiquiti n-modified proteome. (PubMed id 21906983)1 Kim W....Gygi S.P. (2011)
    8. Inhibition of HIV-1 gene expression by Sam68 Delta C: multiple targets but a common mechanism? (PubMed id 19254361)1 Cochrane A. (2009)
    9. Mapping of determinants involved in the stimulation of HIV-1 expression by Sam68. (PubMed id 19091369)1 McLaren M. and Cochrane A. (2009)
    10. Heterogeneous Nuclear Ribonucleoprotein G Regulates Splice Site Selection by Binding to CC(A/C)-rich Regions in Pre-mRNA. (PubMed id 19282290)2 Heinrich B....Stamm S. (2009)

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    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
    About This Section
    Entrez Gene: 202559 HGNC: 18114 AceView: KHDRBS2 Ensembl:ENSG00000112232 euGenes: HUgn202559
    ECgene: KHDRBS2 H-InvDB: KHDRBS2

    (According to HUGE)
    About This Section
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    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
    Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot)
    About This Section
    NameDescription
    PharmGKB entry for KHDRBS2 Pharmacogenomics, SNPs, Pathways

    (Patent information from GeneIP,
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    IP news from LifeMap Sciences, Inc.)
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    Patent Information for KHDRBS2 gene:
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