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    limch1b LIM and calponin homology domains 1b [ Danio rerio (zebrafish) ]

    Gene ID: 557200, updated on 9-Dec-2024

    Summary

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    Official Symbol
    limch1bprovided by ZNC
    Official Full Name
    LIM and calponin homology domains 1bprovided by ZNC
    Primary source
    ZFIN:ZDB-GENE-030131-9210
    See related
    Ensembl:ENSDARG00000103774 AllianceGenome:ZFIN:ZDB-GENE-030131-9210
    Gene type
    protein coding
    RefSeq status
    MODEL
    Organism
    Danio rerio
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes; Danionidae; Danioninae; Danio
    Also known as
    limch1; fc38d05; fk03g12; wu:fc38d05; wu:fk03g12; zgc:175186
    Summary
    Predicted to enable myosin II head/neck binding activity. Predicted to be involved in positive regulation of stress fiber assembly and regulation of focal adhesion assembly. Predicted to be active in stress fiber. Orthologous to human LIMCH1 (LIM and calponin homology domains 1). [provided by Alliance of Genome Resources, Dec 2024]
    Orthologs
    all
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    Genomic context

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    See limch1b in Genome Data Viewer
    Location:
    chromosome: 14
    Exon count:
    30
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCz11 (GCF_000002035.6) 14 NC_007125.7 (16813747..17027395)
    105 previous assembly GRCz10 (GCF_000002035.5) 14 NC_007125.6 (16508122..16721739)

    Chromosome 14 - NC_007125.7Genomic Context describing neighboring genes Neighboring gene T cell immune regulator 1, ATPase H+ transporting V0 subunit a3b Neighboring gene MRN complex interacting protein Neighboring gene uncharacterized LOC137487517 Neighboring gene uncharacterized LOC137487574 Neighboring gene diverse immunoglobulin domain-containing protein 2.1 Neighboring gene diverse immunoglobulin domain-containing protein 2.2

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
    • Description: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
    • BioProject: PRJEB1986
    • Analysis date: Fri Dec 8 19:48:10 2017

    Bibliography

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    Related articles in PubMed

    1. Arap3 is dysregulated in a mouse model of hypotrichosis-lymphedema-telangiectasia and regulates lymphatic vascular development. Kartopawiro J, et al. Hum Mol Genet, 2014 Mar 1. PMID 24163130
    2. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Strausberg RL, et al. Proc Natl Acad Sci U S A, 2002 Dec 24. PMID 12477932, Free PMC Article
    3. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, et al. Brief Bioinform, 2011 Sep. PMID 21873635, Free PMC Article
    4. Gene evolution and gene expression after whole genome duplication in fish: the PhyloFish database. Pasquier J, et al. BMC Genomics, 2016 May 18. PMID 27189481, Free PMC Article

    GeneRIFs: Gene References Into Functions

    General gene information

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    Markers

    Homology

    Clone Names

    • MGC175186

    Gene Ontology Provided by ZFIN

    Function Evidence Code Pubs
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    LIM and calponin homology domains-containing protein 1
    Names
    LIM and calponin homology domains 1

    NCBI Reference Sequences (RefSeq)

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    NEW Try the new Transcript table

    RefSeqs of Annotated Genomes: GCF_000002035.6-RS_2024_08

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCz11 Primary Assembly

    Genomic

    1. NC_007125.7 Reference GRCz11 Primary Assembly

      Range
      16813747..17027395
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_009291003.4 → XP_009289278.1  LIM and calponin homology domains-containing protein 1 isoform X1

      UniProtKB/TrEMBL
      A0A8M3B082, A0A8M9PZJ6
      Conserved Domains (4) summary
      cd00014
      Location:38 → 153
      CH; Calponin homology domain; actin-binding domain which may be present as a single copy or in tandem repeats (which increases binding affinity). The CH domain is found in cytoskeletal and signal transduction proteins, including actin-binding proteins like ...
      pfam00412
      Location:1128 → 1190
      LIM; LIM domain
      pfam15949
      Location:266 → 545
      DUF4757; Domain of unknown function (DUF4757)
      cl20817
      Location:909 → 946
      GBP_C; Guanylate-binding protein, C-terminal domain

    2. XM_068213320.1 → XP_068069421.1  LIM and calponin homology domains-containing protein 1 isoform X3

      UniProtKB/TrEMBL
      A0A8M9QGL6

    3. XM_068213321.1 → XP_068069422.1  LIM and calponin homology domains-containing protein 1 isoform X4

      UniProtKB/TrEMBL
      A0A8M9QPD2

    4. XM_068213319.1 → XP_068069420.1  LIM and calponin homology domains-containing protein 1 isoform X2

      UniProtKB/TrEMBL
      A0A8M9QBD4

    5. XM_068213322.1 → XP_068069423.1  LIM and calponin homology domains-containing protein 1 isoform X5

      UniProtKB/TrEMBL
      A0A8M9QKV9

    6. XM_009291007.4 → XP_009289282.1  LIM and calponin homology domains-containing protein 1 isoform X6

      UniProtKB/TrEMBL
      A0A8M3AHT4, A0A8M9PZJ6
      Conserved Domains (5) summary
      cd00014
      Location:38 → 153
      CH; Calponin homology domain; actin-binding domain which may be present as a single copy or in tandem repeats (which increases binding affinity). The CH domain is found in cytoskeletal and signal transduction proteins, including actin-binding proteins like ...
      PTZ00233
      Location:882 → 1016
      PTZ00233; variable surface protein Vir18; Provisional
      pfam00412
      Location:1013 → 1075
      LIM; LIM domain
      pfam15949
      Location:266 → 430
      DUF4757; Domain of unknown function (DUF4757)
      cl20817
      Location:794 → 831
      GBP_C; Guanylate-binding protein, C-terminal domain

    7. XM_021481138.2 → XP_021336813.1  LIM and calponin homology domains-containing protein 1 isoform X9

      UniProtKB/TrEMBL
      A0A0R4IJJ4, A0A8M9QBD8, A0A8M9QKV9
      Related
      ENSDARP00000134427.1, ENSDART00000161201.2
      Conserved Domains (3) summary
      cd00014
      Location:38 → 153
      CH; Calponin homology domain; actin-binding domain which may be present as a single copy or in tandem repeats (which increases binding affinity). The CH domain is found in cytoskeletal and signal transduction proteins, including actin-binding proteins like ...
      pfam00412
      Location:950 → 1012
      LIM; LIM domain
      pfam15949
      Location:266 → 431
      DUF4757; Domain of unknown function (DUF4757)

    8. XM_009291008.4 → XP_009289283.1  LIM and calponin homology domains-containing protein 1 isoform X7

      UniProtKB/TrEMBL
      A0A8M3ARW6, A0A8M9PZJ6
      Conserved Domains (5) summary
      cd00014
      Location:38 → 153
      CH; Calponin homology domain; actin-binding domain which may be present as a single copy or in tandem repeats (which increases binding affinity). The CH domain is found in cytoskeletal and signal transduction proteins, including actin-binding proteins like ...
      PTZ00233
      Location:870 → 1004
      PTZ00233; variable surface protein Vir18; Provisional
      pfam00412
      Location:1001 → 1063
      LIM; LIM domain
      pfam15949
      Location:266 → 418
      DUF4757; Domain of unknown function (DUF4757)
      cl20817
      Location:782 → 819
      GBP_C; Guanylate-binding protein, C-terminal domain

    9. XM_068213323.1 → XP_068069424.1  LIM and calponin homology domains-containing protein 1 isoform X8

      UniProtKB/TrEMBL
      A0A8M9PZK0

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_001114729.1: Suppressed sequence

      Description
      NM_001114729.1: This RefSeq was suppressed temporarily based on the calculation that the encoded protein was shorter than proteins from the putative ortholog from human: LIMCH1 (GeneID:22998).
    Nucleotide Protein
    Heading Accession and Version

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