WormBase Tree Display for Gene: WBGene00006407

WBGene00006407 Evidence: CGC_data_submission
  SMap: S_parent: Sequence: CHROMOSOME_I
  Identity: Version: 4
    Name: CGC_name: lim-9 Person_evidence: WBPerson54
            WBPerson505
            WBPerson545
      Sequence_name: F25H5.1
      Molecular_name (24)
      Other_name (2)
      Public_name: lim-9
    DB_info: Database: AceView gene 1J758
        WormQTL gene WBGene00006407
        WormFlux gene WBGene00006407
        NDB locus_tag CELE_F25H5.1
        Panther gene CAEEL|WormBase=F25H5.1i|UniProtKB=A0A0K3AQM0
          family PTHR24205
        NCBI gene 3565712
        RefSeq protein NM_001377616.3
            NM_001026238.6
            NM_001377617.3
            NM_001026237.7
            NM_001313465.3
            NM_001313491.3
            NM_001030057.5
            NM_001313466.5
        TREEFAM TREEFAM_ID TF321684
        TrEMBL UniProtAcc G5EDJ5
            A0A0K3AQM0
            Q3S1I9
            A0A0K3AQP4
            O17833
            G5EEA4
            A0A0K3ATK8
            G5EF39
        UniProt_GCRP UniProtAcc A0A0K3AQM0
    Species: Caenorhabditis elegans
    History: Version_change: 1 07 Apr 2004 11:29:40 WBPerson1971 Event: Imported: Initial conversion from geneace
        2 02 Feb 2007 10:20:45 WBPerson2970 Name_change: CGC_name: lim-9
                Other_name: tag-15
        3 10 Jun 2014 12:12:12 WBPerson1983 Event: Acquires_merge: WBGene00008108
        4 13 Nov 2014 15:02:41 WBPerson4025 Event: Acquires_merge: WBGene00008109
      Acquires_merge: WBGene00008108
        WBGene00008109
    Status: Live
  Gene_info: Biotype: SO:0001217
    Gene_class: lim
    Allele (432)
    Strain: WBStrain00035585
      WBStrain00035699
    In_cluster: conserved_miRNA_siRNA_cluster
    RNASeq_FPKM (74)
    GO_annotation: 00000569
      00000570
      00000571
      00000572
      00000573
      00014123
      00014124
      00014125
      00014126
      00114034
    Ortholog: WBGene00060910 Caenorhabditis remanei From_analysis: OMA
            TreeFam
            Inparanoid_8
            WormBase-Compara
      WBGene00036743 Caenorhabditis briggsae From_analysis: OrthoMCL
            WormBase-Compara
      WBGene00145437 Caenorhabditis brenneri From_analysis: OMA
            TreeFam
            Inparanoid_8
            WormBase-Compara
      WBGene00157611 Caenorhabditis brenneri From_analysis: TreeFam
            WormBase-Compara
      WBGene00153748 Caenorhabditis brenneri From_analysis: Inparanoid_8
      WBGene00143684 Caenorhabditis brenneri From_analysis: Inparanoid_8
      WBGene00130903 Caenorhabditis japonica From_analysis: Inparanoid_8
      WBGene00060913 Caenorhabditis remanei From_analysis: Inparanoid_8
      WBGene00223850 Brugia malayi From_analysis: WormBase-Compara
      CBOVI.g12141 Caenorhabditis bovis From_analysis: WormBase-Compara
      CSP21.g5419 Caenorhabditis parvicauda From_analysis: WormBase-Compara
      CSP26.g8009 Caenorhabditis zanzibari From_analysis: WormBase-Compara
      CSP28.g17844 Caenorhabditis panamensis From_analysis: WormBase-Compara
      CSP29.g10904 Caenorhabditis becei From_analysis: WormBase-Compara
      CSP31.g4289 Caenorhabditis uteleia From_analysis: WormBase-Compara
      CSP32.g6557 Caenorhabditis sulstoni From_analysis: WormBase-Compara
      CSP38.g598 Caenorhabditis quiockensis From_analysis: WormBase-Compara
      CSP39.g5378 Caenorhabditis waitukubuli From_analysis: WormBase-Compara
      CSP40.g4492 Caenorhabditis tribulationis From_analysis: WormBase-Compara
      Cang_2012_03_13_00001.g94 Caenorhabditis angaria From_analysis: WormBase-Compara
      Cang_2012_03_13_00001.g95 Caenorhabditis angaria From_analysis: WormBase-Compara
      Cnig_chr_I.g344 Caenorhabditis nigoni From_analysis: WormBase-Compara
      Cnig_chr_I.g345 Caenorhabditis nigoni From_analysis: WormBase-Compara
      Csp11.Scaffold629.g9828 Caenorhabditis tropicalis From_analysis: WormBase-Compara
      Csp11.Scaffold629.g9829 Caenorhabditis tropicalis From_analysis: WormBase-Compara
      Csp5_scaffold_04025.g31864 Caenorhabditis sinica From_analysis: WormBase-Compara
      Csp5_scaffold_04265.g32495 Caenorhabditis sinica From_analysis: WormBase-Compara
      FL83_21207 Caenorhabditis latens From_analysis: WormBase-Compara
      FL83_21208 Caenorhabditis latens From_analysis: WormBase-Compara
      GCK72_001430 Caenorhabditis remanei From_analysis: WormBase-Compara
      GCK72_001431 Caenorhabditis remanei From_analysis: WormBase-Compara
      OTIPU.nOt.2.0.1.g12008 Oscheius tipulae From_analysis: WormBase-Compara
      Pan_g14180 Panagrellus redivivus From_analysis: WormBase-Compara
      Sp34_10112700 Caenorhabditis inopinata From_analysis: WormBase-Compara
      Sp34_10112800 Caenorhabditis inopinata From_analysis: WormBase-Compara
      chrI_pilon.g1761 Caenorhabditis elegans From_analysis: WormBase-Compara
      WBGene00209538 Caenorhabditis japonica From_analysis: WormBase-Compara
      WBGene00237779 Onchocerca volvulus From_analysis: WormBase-Compara
      WBGene00096292 Pristionchus pacificus From_analysis: WormBase-Compara
      WBGene00261627 Strongyloides ratti From_analysis: WormBase-Compara
      WBGene00289416 Trichuris muris From_analysis: WormBase-Compara
      ZFIN:ZDB-GENE-040808-49 Danio rerio From_analysis: EnsEMBL-Compara
            OrthoFinder
            OrthoInspector
            Panther
            PhylomeDB
            SonicParanoid
      ZFIN:ZDB-GENE-040822-3 Danio rerio From_analysis: EnsEMBL-Compara
            OrthoFinder
            OrthoInspector
            Panther
            SonicParanoid
      ZFIN:ZDB-GENE-041010-121 Danio rerio From_analysis: EnsEMBL-Compara
            OrthoFinder
            OrthoInspector
            Panther
            PhylomeDB
            SonicParanoid
      ZFIN:ZDB-GENE-030131-8356 Danio rerio From_analysis: EnsEMBL-Compara
            OrthoFinder
            Panther
            PhylomeDB
      ZFIN:ZDB-GENE-030131-4741 Danio rerio From_analysis: EnsEMBL-Compara
            OrthoFinder
            OrthoInspector
            Panther
            SonicParanoid
      HGNC:3703 Homo sapiens From_analysis: EnsEMBL-Compara
            OrthoFinder
            OrthoInspector
            Panther
            PhylomeDB
            SonicParanoid
      HGNC:3704 Homo sapiens From_analysis: EnsEMBL-Compara
            OrthoFinder
            OrthoInspector
            Panther
            PhylomeDB
      HGNC:17371 Homo sapiens From_analysis: EnsEMBL-Compara
            OrthoFinder
            Panther
            PhylomeDB
            SonicParanoid
      MGI:1338762 Mus musculus From_analysis: EnsEMBL-Compara
            OrthoFinder
            OrthoInspector
            Panther
            PhylomeDB
            SonicParanoid
      MGI:1341092 Mus musculus From_analysis: EnsEMBL-Compara
            OrthoFinder
            Panther
            PhylomeDB
      MGI:1913192 Mus musculus From_analysis: EnsEMBL-Compara
            OrthoFinder
            OrthoInspector
            Panther
            SonicParanoid
      RGD:61963 Rattus norvegicus From_analysis: EnsEMBL-Compara
            OrthoFinder
            OrthoInspector
            Panther
            PhylomeDB
            SonicParanoid
      RGD:1307056 Rattus norvegicus From_analysis: EnsEMBL-Compara
            OrthoFinder
            OrthoInspector
            Panther
            SonicParanoid
      RGD:1307180 Rattus norvegicus From_analysis: EnsEMBL-Compara
            OrthoFinder
            Panther
            PhylomeDB
    Structured_description: Concise_description: lim-9 encodes a protein containing one PET domain and six LIM domains and is orthologous to Drosophila LIMPET and vertebrate FHL2; in vitro binding and yeast two-hybrid assays indicate that LIM-9 physically interacts with UNC-96 and UNC-97 and thus, is likely a component of a protein complex that links muscle focal adhesions to thick filaments; LIM-9 also enables Wnt-directed planar cell polarity and is required for the fully asymmetrical division of B.a versus B.p cells, though this requirement is quantitatively weak; a lim-9::gfp promoter fusion is expressed in pharyngeal and body wall muscles, as well as in some neuronal processes, vulva, spermathecae, anal sphincter and depressor muscles, gonadal sheath, and the excretory canal; staining with LIM-9 antibodies reveals that in body wall muscle LIM-9 localizes, at least partially, to M-lines, around which myosin thick filaments are organized. Paper_evidence: WBPaper00027345
            WBPaper00030924
          Curator_confirmed: WBPerson1843
            WBPerson567
          Date_last_updated: 27 Feb 2009 00:00:00
      Automated_description: Enables protein domain specific binding activity. Predicted to be involved in regulation of DNA-templated transcription. Located in M band. Expressed in several structures, including body wall musculature; excretory canal; non-striated muscle; spermatheca; and vulva. Is an ortholog of human FHL2 (four and a half LIM domains 2). Paper_evidence: WBPaper00065943
          Curator_confirmed: WBPerson324
            WBPerson37462
          Inferred_automatically: This description was generated automatically by a script based on data from the WS291 version of WormBase
          Date_last_updated: 29 Nov 2023 00:00:00
  Molecular_info: Corresponding_CDS: F25H5.1b
      F25H5.1c
      F25H5.1d
      F25H5.1e
      F25H5.1f
      F25H5.1g
      F25H5.1h
      F25H5.1i
    Corresponding_CDS_history: F25H5.1a:wp136
      F25H5.1a:wp275
      F25H5.1b:wp136
      F25H5.1b:wp246
      F25H5.1c:wp246
      F25H5.1d:wp246
      F25H5.1f:wp183
    Corresponding_transcript: F25H5.1b.1
      F25H5.1c.1
      F25H5.1d.1
      F25H5.1e.1
      F25H5.1f.1
      F25H5.1g.1
      F25H5.1h.1
      F25H5.1i.1
    Other_sequence (62)
    Associated_feature (44)
    Transcription_factor: WBTranscriptionFactor000581
  Experimental_info: RNAi_result (14)
    Expr_pattern: Expr8313
      Expr8316
      Expr8552
      Expr1025302
      Expr1029193
      Expr1032599
      Expr1146521
      Expr1149460
      Expr2013155
      Expr2031387
    Drives_construct: WBCnstr00013257
    Antibody: WBAntibody00001285
    Microarray_results (81)
    Expression_cluster (241)
    Interaction (40)
  Map_info: Map: I Position: 3.6557 Error: 0.004609
    Positive: Positive_clone: F25H5 Inferred_automatically: From sequence, transcript, pseudogene data
    Pseudo_map_position
  Reference (13)
  Remark: Gene name created from parsing 'genotype' field from CGC strain information CGC_data_submission
    Map position created from combination of previous interpolated map position (based on known location of sequence) and allele information. Therefore this is not a genetic map position based on recombination frequencies or genetic experiments. This was done on advice of the CGC. CGC_data_submission
    [140610 pad] Gene was missing Acquires_merge Event history data so inferred from Acquires_merge tag.
  Method: Gene