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

Gene ID: 557200, updated on 27-Mar-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, Apr 2022]
Orthologs
all
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Genomic context

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Location:
chromosome: 14
Exon count:
30
Annotation release Status Assembly Chr Location
106 current GRCz11 (GCF_000002035.6) 14 NC_007125.7 (16813762..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 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
  
enables myosin II head/neck binding IBA
Inferred from Biological aspect of Ancestor
more info
  
Process Evidence Code Pubs
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 1
Names
LIM and calponin homology domains 1

NCBI Reference Sequences (RefSeq)

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RefSeqs of Annotated Genomes: Danio rerio Annotation Release 106 details...Open this link in a new tab

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
    16813762..17027395
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_021481134.1 → XP_021336809.1  LIM and calponin homology domains-containing protein 1 isoform X4

    UniProtKB/TrEMBL
    A0A8M9QGL6
    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:1112 → 1174
    LIM; LIM domain
    pfam15949
    Location:266 → 558
    DUF4757; Domain of unknown function (DUF4757)
    cl20817
    Location:921 → 958
    GBP_C; Guanylate-binding protein, C-terminal domain

  2. XM_021481132.1 → XP_021336807.1  LIM and calponin homology domains-containing protein 1 isoform X1

    UniProtKB/TrEMBL
    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:1140 → 1202
    LIM; LIM domain
    pfam15949
    Location:266 → 558
    DUF4757; Domain of unknown function (DUF4757)
    cl20817
    Location:921 → 958
    GBP_C; Guanylate-binding protein, C-terminal domain

  3. XM_021481135.1 → XP_021336810.1  LIM and calponin homology domains-containing protein 1 isoform X5

    UniProtKB/TrEMBL
    A0A8M9QPD2
    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:1102 → 1164
    LIM; LIM domain
    pfam15949
    Location:266 → 558
    DUF4757; Domain of unknown function (DUF4757)

  4. XM_021481133.1 → XP_021336808.1  LIM and calponin homology domains-containing protein 1 isoform X3

    UniProtKB/TrEMBL
    A0A8M9QBD4
    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:1115 → 1177
    LIM; LIM domain
    pfam15949
    Location:266 → 558
    DUF4757; Domain of unknown function (DUF4757)
    cl20817
    Location:896 → 933
    GBP_C; Guanylate-binding protein, C-terminal domain

  5. XM_009291003.3 → XP_009289278.1  LIM and calponin homology domains-containing protein 1 isoform X2

    UniProtKB/TrEMBL
    A0A8M3B082
    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

  6. XM_021481136.1 → XP_021336811.1  LIM and calponin homology domains-containing protein 1 isoform X6

    UniProtKB/TrEMBL
    A0A8M9QKV9
    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:1077 → 1139
    LIM; LIM domain
    pfam15949
    Location:266 → 558
    DUF4757; Domain of unknown function (DUF4757)

  7. XM_009291007.3 → XP_009289282.1  LIM and calponin homology domains-containing protein 1 isoform X7

    UniProtKB/TrEMBL
    A0A8M3AHT4
    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

  8. XM_009291008.3 → XP_009289283.1  LIM and calponin homology domains-containing protein 1 isoform X8

    UniProtKB/TrEMBL
    A0A8M3ARW6
    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_021481138.1 → XP_021336813.1  LIM and calponin homology domains-containing protein 1 isoform X10

    UniProtKB/TrEMBL
    A0A0R4IJJ4, A0A8M9QBD8
    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)

  10. XM_021481137.1 → XP_021336812.1  LIM and calponin homology domains-containing protein 1 isoform X9

    UniProtKB/TrEMBL
    A0A8M9PZK0
    Conserved Domains (3) summary
    pfam00412
    Location:966 → 1028
    LIM; LIM domain
    pfam15949
    Location:92 → 384
    DUF4757; Domain of unknown function (DUF4757)
    cl20817
    Location:747 → 784
    GBP_C; Guanylate-binding protein, C-terminal domain

RNA

  1. XR_002459941.1 RNA Sequence

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
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