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limch1a LIM and calponin homology domains 1a [ Danio rerio (zebrafish) ]

Gene ID: 561940, updated on 28-Oct-2024

Summary

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Official Symbol
limch1aprovided by ZNC
Official Full Name
LIM and calponin homology domains 1aprovided by ZNC
Primary source
ZFIN:ZDB-GENE-090312-153
See related
Ensembl:ENSDARG00000074275 AllianceGenome:ZFIN:ZDB-GENE-090312-153
Gene type
protein coding
RefSeq status
PROVISIONAL
Organism
Danio rerio
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes; Danionidae; Danioninae; Danio
Also known as
si:ch211-157h5.2
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 act upstream of or within actomyosin structure organization. Predicted to be active in stress fiber. Is expressed in trunk vasculature. Orthologous to human LIMCH1 (LIM and calponin homology domains 1). [provided by Alliance of Genome Resources, Oct 2024]
Orthologs
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Genomic context

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See limch1a in Genome Data Viewer
Location:
chromosome: 1
Exon count:
34
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCz11 (GCF_000002035.6) 1 NC_007112.7 (18965655..19070270)
105 previous assembly GRCz10 (GCF_000002035.5) 1 NC_007112.6 (18272658..18373790)

Chromosome 1 - NC_007112.7Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC137495484 Neighboring gene uncharacterized LOC137495116 Neighboring gene uncharacterized LOC137495485 Neighboring gene paired like homeobox 2Ba Neighboring gene exosome component 9

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 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. In vivo proteomic mapping through GFP-directed proximity-dependent biotin labelling in zebrafish. Xiong Z, et al. Elife, 2021 Feb 16. PMID 33591275, Free PMC Article
  3. 15000 unique zebrafish EST clusters and their future use in microarray for profiling gene expression patterns during embryogenesis. Lo J, et al. Genome Res, 2003 Mar. PMID 12618376, Free PMC Article
  4. Evolution of complexity in the zebrafish synapse proteome. Bayés À, et al. Nat Commun, 2017 Mar 2. PMID 28252024, Free PMC Article
  5. RFX transcription factors are essential for hearing in mice. Elkon R, et al. Nat Commun, 2015 Oct 15. PMID 26469318, Free PMC Article

See all (7) citations in PubMed

GeneRIFs: Gene References Into Functions

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Gene Ontology Provided by ZFIN

Function Evidence Code Pubs
enables actin binding IEA
Inferred from Electronic Annotation
more info
  
enables metal ion binding IEA
Inferred from Electronic Annotation
more info
  
enables myosin II head/neck binding IBA
Inferred from Biological aspect of Ancestor
more info
  
Process Evidence Code Pubs
acts_upstream_of_or_within actomyosin structure organization IEA
Inferred from Electronic Annotation
more info
  
involved_in positive regulation of stress fiber assembly IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in regulation of focal adhesion assembly IBA
Inferred from Biological aspect of Ancestor
more info
  
Component Evidence Code Pubs
is_active_in stress fiber IBA
Inferred from Biological aspect of Ancestor
more info
  

General protein information

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

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

  1. NM_001145577.1 → NP_001139049.1  LIM and calponin homology domains-containing protein 1a isoform 2

    Status: PROVISIONAL

    Source sequence(s)
    BX323984
    UniProtKB/TrEMBL
    A0A8M1NT62, B8A4X7
    Related
    ENSDARP00000120339.1, ENSDART00000132379.2
    Conserved Domains (4) summary
    cd00014
    Location:27 → 107
    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:949 → 1011
    LIM; LIM domain
    pfam15949
    Location:247 → 404
    DUF4757; Domain of unknown function (DUF4757)
    cl20817
    Location:726 → 761
    GBP_C; Guanylate-binding protein, C-terminal domain

  2. NM_001430852.1 → NP_001417781.1  LIM and calponin homology domains-containing protein 1a isoform 1

    Status: PROVISIONAL

    Source sequence(s)
    BX323984

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_007112.7 Reference GRCz11 Primary Assembly

    Range
    18965655..19070270
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_068219969.1 → XP_068076070.1  LIM and calponin homology domains-containing protein 1a isoform X1

  2. XM_068219970.1 → XP_068076071.1  LIM and calponin homology domains-containing protein 1a isoform X3

  3. XM_068219973.1 → XP_068076074.1  LIM and calponin homology domains-containing protein 1a isoform X4

  4. XM_021475267.2 → XP_021330942.1  LIM and calponin homology domains-containing protein 1a isoform X2

    UniProtKB/TrEMBL
    A0A8M9PHW0
    Conserved Domains (3) summary
    cd00014
    Location:27 → 107
    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:1890 → 1952
    LIM; LIM domain
    pfam15949
    Location:1166 → 1308
    DUF4757; Domain of unknown function (DUF4757)

  5. XM_021475273.2 → XP_021330948.1  LIM and calponin homology domains-containing protein 1a isoform X6

    UniProtKB/TrEMBL
    A0A8M9PV51
    Conserved Domains (3) summary
    cd00014
    Location:27 → 107
    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:1774 → 1836
    LIM; LIM domain
    pfam15949
    Location:1050 → 1192
    DUF4757; Domain of unknown function (DUF4757)

  6. XM_021475270.2 → XP_021330945.1  LIM and calponin homology domains-containing protein 1a isoform X5

    UniProtKB/TrEMBL
    A0A8M9QBW7
    Conserved Domains (3) summary
    cd00014
    Location:27 → 107
    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:1784 → 1846
    LIM; LIM domain
    pfam15949
    Location:1060 → 1202
    DUF4757; Domain of unknown function (DUF4757)

  7. XM_021475278.2 → XP_021330953.1  LIM and calponin homology domains-containing protein 1a isoform X7

    UniProtKB/TrEMBL
    A0A8M9PV53
    Conserved Domains (4) summary
    cd00014
    Location:27 → 107
    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:1502 → 1564
    LIM; LIM domain
    pfam15949
    Location:778 → 920
    DUF4757; Domain of unknown function (DUF4757)
    cl20817
    Location:1279 → 1314
    GBP_C; Guanylate-binding protein, C-terminal domain
Nucleotide Protein
Heading Accession and Version

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