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RTKN2 Gene

protein-coding   GIFtS: 52
GCID: GC10M063942

Rhotekin 2

(Previous names: pleckstrin homology domain containing, family K member 1)
(Previous symbol: PLEKHK1)
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(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
Rhotekin 21 2     PH Domain-Containing Family K Member 12 3
PLEKHK11 2 3     bA531F24.12
Pleckstrin Homology Domain Containing, Family K Member 11 2     rhotekin-22
Pleckstrin Homology Domain-Containing Family K Member 12 3     

External Ids:    HGNC: 193641   Entrez Gene: 2197902   Ensembl: ENSG000001820107   UniProtKB: Q8IZC43   

Export aliases for RTKN2 gene to outside databases

Previous GC identifers: GC10M063035 GC10M063835 GC10M063613 GC10M057942


(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 RTKN2 Gene:
RTKN2 (rhotekin 2) is a protein-coding gene. GO annotations related to this gene include phospholipid binding. An important paralog of this gene is RTKN.

UniProtKB/Swiss-Prot: RTKN2_HUMAN, Q8IZC4
Function: May play an important role in lymphopoiesis




(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_000010.10  NT_030059.14  NC_018921.2  
Regulatory elements:
   Regulatory transcription factor binding sites in the RTKN2 gene promoter:
         Pbx1a   Pax-6   HTF   HSF1 (long)   Meis-1b   S8   FOXO4   HSF1short   Meis-1a   Meis-1   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidRTKN2 promoter sequence
   Search Chromatin IP Primers for RTKN2

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat RTKN2


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

Entrez Gene cytogenetic band: 10q21.2   Ensembl cytogenetic band:  10q21.2   HGNC cytogenetic band: 10q21.3

RTKN2 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
RTKN2 gene location

GeneLoc information about chromosome 10         GeneLoc Exon Structure

GeneLoc location for GC10M063942:  view genomic region     (about GC identifiers)

Start:
63,942,794 bp from pter      End:
64,028,466 bp from pter
Size:
85,673 bases      Orientation:
minus 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., eBioscience, and/or antibodies-online,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, Cloud-Clone Corp., eBioscience, and/or antibodies-online, Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, Abcam, Cloud-Clone Corp, antibodies-online, and/or others.)
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UniProtKB/Swiss-Prot: RTKN2_HUMAN, Q8IZC4 (See protein sequence)
Recommended Name: Rhotekin-2  
Size: 609 amino acids; 69304 Da
Sequence caution: Sequence=BAC04837.1; Type=Erroneous initiation; Sequence=BC048002; Type=Miscellaneous
discrepancy; Note=Intron retention;
Secondary accessions: Q3ZCR1 Q68DZ6 Q8N8K1 Q8TAV2
Alternative splicing: 3 isoforms:  Q8IZC4-1   Q8IZC4-2   Q8IZC4-3   (No experimental confirmation available)

Explore the universe of human proteins at neXtProt for RTKN2: NX_Q8IZC4

Explore proteomics data for RTKN2 at MOPED

Post-translational modifications: 

  • Modification sites at neXtProt
  • Modification sites at PhosphoSitePlus

  • See RTKN2 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins (2 alternative transcripts): 
    NP_001269870.1  NP_660350.2  

    ENSEMBL proteins: 
     ENSP00000325379   ENSP00000362894   ENSP00000378678   ENSP00000378682  

    RTKN2 Human Recombinant Protein Products:

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    Cloud-Clone Corp. Proteins for RTKN2

     
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    antibodies-online proteins for RTKN2 (5 products) 

     
    antibodies-online peptides for RTKN2

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    antibodies-online antibodies for RTKN2 (18 products) 

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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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    HGNC Gene Families:
    PLEKH: Pleckstrin homology (PH) domain containing

    4 InterPro protein domains:
     IPR011072 HR1_rho-bd
     IPR001849 Pleckstrin_homology
     IPR011993 PH_like_dom
     IPR012966 DUF1709

    Graphical View of Domain Structure for InterPro Entry Q8IZC4

    ProtoNet protein and cluster: Q8IZC4

    2 Blocks protein domains:
    IPB001849 Pleckstrin-like
    IPB011072 Protein kinase PKN/PRK1


    UniProtKB/Swiss-Prot: RTKN2_HUMAN, Q8IZC4
    Similarity: Contains 1 PH domain


    Find genes that share domains with RTKN2           About GenesLikeMe


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, 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:

         UniProtKB/Swiss-Prot Summary: RTKN2_HUMAN, Q8IZC4
    Function: May play an important role in lymphopoiesis
    Induction: Up-regulated in cells resistant to 25-hydroxy cholesterol (25-OHC). Down-regulated in lymphocytes
    activated by treatment with phytohemagglutinin (PHA)

    Animal Models:

       genOway: Develop your customized and physiologically relevant rodent model for RTKN2

    miRNA
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    miRTarBase miRNAs that target RTKN2:
    hsa-mir-10a-5p (MIRT047538), hsa-mir-193b-3p (MIRT016449), hsa-mir-10b-5p (MIRT047409), hsa-mir-92b-3p (MIRT040583), hsa-mir-192-5p (MIRT026703), hsa-mir-215-5p (MIRT024839)

    Block miRNA regulation of human, mouse, rat RTKN2 using miScript Target Protectors
    Selected qRT-PCR Assays for microRNAs that regulate RTKN2 (see all 68):
    hsa-miR-640 hsa-miR-30d hsa-miR-374a hsa-miR-578 hsa-miR-30a hsa-miR-3613-3p hsa-miR-3174 hsa-miR-3688-3p
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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 COMPARTMENTS: 

    CompartmentConfidence
    cytosol3
    mitochondrion2
    nucleus2
    plasma membrane2

    Gene Ontology (GO): 1 cellular component term:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005886plasma membrane IEA--

    Find genes that share ontologies with RTKN2           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 RTKN2
    Interactions:

        Search GeneGlobe Interaction Network for RTKN2

    STRING Interaction Network Preview (showing 2 interactants - click image to see more details)

    3 Interacting proteins for RTKN2 (Q8IZC42, 3 ENSP000003628944) via UniProtKB, MINT, STRING, and/or I2D
    InteractantInteraction Details
    GeneCardExternal ID(s)
    PACSIN1Q9BY113, ENSP000002444584I2D: score=3 STRING: ENSP00000244458
    IGHG1P018573, ENSP000003749904I2D: score=1 STRING: ENSP00000374990
    --P310162MINT-8108746
    About this table

    Gene Ontology (GO): 3 biological process terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0007165signal transduction IEA--
    GO:0008284positive regulation of cell proliferation IEA--
    GO:0030097hemopoiesis IEA--

    Find genes that share ontologies with RTKN2           About GenesLikeMe



    (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 RTKN2



    (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 RTKN2 gene (2 alternative transcripts): 
    NM_001282941.1  NM_145307.3  

    Unigene Cluster for RTKN2:

    Rhotekin 2
    Hs.58559  [show with all ESTs]
    Unigene Representative Sequence: NM_145307
    4 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000315289(uc009xpf.1) ENST00000373789(uc001jlv.3 uc001jlw.3)
    ENST00000395260(uc001jlx.2) ENST00000395265
    miRNA
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    Selected qRT-PCR Assays for microRNAs that regulate RTKN2 (see all 68):
    hsa-miR-640 hsa-miR-30d hsa-miR-374a hsa-miR-578 hsa-miR-30a hsa-miR-3613-3p hsa-miR-3174 hsa-miR-3688-3p
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    Pre-validated RT2 qPCR Primer Assay in human, mouse, rat RTKN2
      QuantiTect SYBR Green Assays in human, mouse, rat RTKN2
      QuantiFast Probe-based Assays in human, mouse, rat RTKN2

    Additional mRNA sequence: 

    AK096671.1 AY150309.1 BC025765.1 BC141821.1 BC142725.1 CR749217.1 

    6 DOTS entries:

    DT.97781996  DT.75174970  DT.97817991  DT.92056662  DT.86846523  DT.95225269 

    Selected AceView cDNA sequences (see all 46):

    AA744789 AI682623 AI355843 CA437443 AW262908 AA761494 CR749217 AW470128 
    BM682640 CA438324 BM993301 AW665138 NM_145307 BX330889 BG029885 CB114709 
    BM993547 AW291786 AI028232 BC048002 BF968275 AY150309 BM723441 AK096671 

    GeneLoc Exon Structure

    5 Alternative Splicing Database (ASD) splice patterns (SP) for RTKN2    About this scheme

    ExUns: 1a · 1b · 1c ^ 2 ^ 3 ^ 4 ^ 5a · 5b · 5c ^ 6a · 6b ^ 7 ^ 8 ^ 9 ^ 10 ^ 11 ^ 12 ^ 13 ^ 14a · 14b · 14c
    SP1:                                            -     -                                   -     -                                 
    SP2:                                                                                            -                                 
    SP3:                                                                                                                              
    SP4:                          -                                                                                                   
    SP5:                                                                                                                              


    ECgene alternative splicing isoforms for RTKN2

    (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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    RTKN2 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: --
    RTKN2 Expression
    About this image

    RTKN2 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    RTKN2 Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.58559

    UniProtKB/Swiss-Prot: RTKN2_HUMAN, Q8IZC4
    Tissue specificity: Expressed in lymphocytes, CD4 positive T-cells and bone marrow-derived cells. Also expressed
    in lung, colon, thymus and brain

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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 RTKN2 gene from Selected species (see all 13)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Rtkn21 , 5 rhotekin 21, 5 77.44(n)1
    74.17(a)1
      10 (35.06 cM)5
    1707991  NM_001081346.11  NP_001074815.11 
     679795705 
    chicken
    (Gallus gallus)
    Aves RTKN21 rhotekin 2 73.12(n)
    68.32(a)
      423660  NM_001199597.1  NP_001186526.1 
    lizard
    (Anolis carolinensis)
    Reptilia RTKN26
    rhotekin 2
    59(a)
    1 ↔ 1
    GL343204.1(2958326-3008993)
    African clawed frog
    (Xenopus laevis)
    Amphibia Xl.325142 Xenopus laevis transcribed sequences 75.94(n)    BJ619262.1 
    zebrafish
    (Danio rerio)
    Actinopterygii wufl63a032 wufl63a03 70.9(n)   386821  57056939 
    worm
    (Caenorhabditis elegans)
    Secernentea C07B5.46
    Protein C07B5.4, isoform a
    20(a)
    1 → many
    X(9529533-9536634) WBGene00007409


    ENSEMBL Gene Tree for RTKN2 (if available)
    TreeFam Gene Tree for RTKN2 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for RTKN2 gene
    RTKN2  
    1 SIMAP similar gene for RTKN2 using alignment to 2 protein entries:     RTKN2_HUMAN (see all proteins):
    RTKN

    Find genes that share paralogs with RTKN2           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 RTKN2 (see all 1437)    About this table                                 

    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 10 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs14324111,2
    C,F,A,H--63952639(+) AAGCAT/CATTTT 1 -- int125Minor allele frequency- C:0.33NS EA NA WA CSA 2478
    rs1440781711,2
    --63952972(+) AACAAC/TTTATT 1 -- ut310--------
    rs1865718781,2
    --63953067(+) TACCAC/TGTCTC 1 -- ut310--------
    rs1898461091,2
    --63953078(+) AAGAGA/CAAACT 1 -- ut310--------
    rs1502813211,2
    --63953139(+) ATTATC/TAAACG 1 -- ut310--------
    rs1379008081,2
    C--63953218(+) TTTGTC/TGTTAA 1 -- ut310--------
    rs1823848241,2
    --63953382(+) TCCCCA/CACTCT 1 -- ut310--------
    rs1149816781,2
    C,F--63953457(+) AGTAGC/TGACTG 1 -- ut311Minor allele frequency- T:0.04WA 118
    rs1879075921,2
    --63953770(+) ATCAGA/TTCTTT 1 -- ut310--------
    rs412740561,2
    --63953779(+) TTTAAC/TGTACA 1 -- ut310--------

    HapMap Linkage Disequilibrium report for RTKN2 (63942794 - 64028466 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 7 variations for RTKN2:    About this table    
    Variant IDTypeSubtypePubMed ID
    esv2737551CNV Deletion23290073
    esv2737540CNV Deletion23290073
    nsv6831CNV Insertion18451855
    esv34099CNV Loss18971310
    nsv467292CNV Loss19166990
    nsv8681CNV Gain18304495
    nsv831890CNV Gain17160897

    Human Gene Mutation Database (HGMD): RTKN2
    Site Specific Mutation Identification with PCR Assays
    SeqTarget long-range PCR primers for resequencing RTKN2
    DNA2.0 Custom Variant and Variant Library Synthesis for RTKN2

    (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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    Find genes that share disorders with RTKN2           About GenesLikeMe

    Genetic Association Database (GAD): RTKN2
    Human Genome Epidemiology (HuGE) Navigator: RTKN2 (1 document)

    Export disorders for RTKN2 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 RTKN2 gene, integrated from 10 sources (see all 16):
    (articles sorted by number of sources associating them with RTKN2)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Identification and characterization of a lymphocytic Rho-GTPase effector: rhotekin-2. (PubMed id 15504364)1, 2, 3, 9 Collier F.M....Kirkland M.A. (Biochem. Biophys. Res. Commun. 2004)
    2. Genome-wide association study identifies eight loci associated with blood pressure. (PubMed id 19430483)1, 4 Newton-Cheh C....Munroe P.B. (Nat. Genet. 2009)
    3. A scan of chromosome 10 identifies a novel locus showing strong association with late-onset Alzheimer disease. (PubMed id 16385451)1, 4 Grupe A....Goate A. (Am. J. Hum. Genet. 2006)
    4. Mechanisms of resistance to the cytotoxic effects of oxysterols in human leukemic cells. (PubMed id 15120425)1, 2 Gregorio-King C.C.... Kirkland M.A. (J. Steroid Biochem. Mol. Biol. 2004)
    5. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1, 2 Ota T.... Sugano S. (Nat. Genet. 2004)
    6. Pathway Analysis of ChIP-Seq-Based NRF1 Target Genes Suggests a Logical Hypothesis of their Involvement in the Pathogenesis of Neurodegenerative Diseases. (PubMed id 24250222)1 Satoh J....Yamamoto Y. (Gene Regul Syst Bio 2013)
    7. Meta-analysis followed by replication identifies loci in or near CDKN1B, TET3, CD80, DRAM1, and ARID5B as associated with systemic lupus erythematosus in Asians. (PubMed id 23273568)1 Yang W....Lau Y.L. (Am. J. Hum. Genet. 2013)
    8. Functional variants in NFKBIE and RTKN2 involved in activation of the NF-I_B pathway are associated with rheumatoid arthritis in Japanese. (PubMed id 23028356)1 Myouzen K....Yamamoto K. (PLoS Genet. 2012)
    9. Charting the landscape of tandem BRCT domain-mediated protein interactions. (PubMed id 22990118)1 Woods N.T....Monteiro A.N. (Sci Signal 2012)
    10. The SH3 domain of postsynaptic density 95 mediates inflammatory pain through phosphatidylinositol-3-kinase recruitment. (PubMed id 20467438)1 Arbuckle M.I....Grant S.G. (EMBO Rep. 2010)

    (in PubMed, OMIM, and NCBI Bookshelf)
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      Query String
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      (Note: In FireFox, select the above section and copy using Ctrl-C)

    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
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    Entrez Gene: 219790 HGNC: 19364 AceView: PLEKHK1 Ensembl:ENSG00000182010 euGenes: HUgn219790
    ECgene: RTKN2 H-InvDB: RTKN2

    (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)
    About This Section

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    NameDescription
    PharmGKB entry for RTKN2 Pharmacogenomics, SNPs, Pathways

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
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    Patent Information for RTKN2 gene:
    Search GeneIP for patents involving RTKN2

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



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