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    cmn calymmin [ Danio rerio (zebrafish) ]

    Gene ID: 30208, updated on 12-May-2024

    Summary

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    Official Symbol
    cmnprovided by ZNC
    Official Full Name
    calymminprovided by ZNC
    Primary source
    ZFIN:ZDB-GENE-000208-9
    See related
    Ensembl:ENSDARG00000055527 AllianceGenome:ZFIN:ZDB-GENE-000208-9
    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
    wu:fd07b03
    Summary
    Acts upstream of or within embryonic skeletal system development. Located in collagen-containing extracellular matrix. Is expressed in notochord and notochord posterior region. [provided by Alliance of Genome Resources, Apr 2022]
    Orthologs
    all
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    Genomic context

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    See cmn in Genome Data Viewer
    Location:
    chromosome: 12
    Exon count:
    56
    Annotation release Status Assembly Chr Location
    106 current GRCz11 (GCF_000002035.6) 12 NC_007123.7 (13118545..13164249)
    105 previous assembly GRCz10 (GCF_000002035.5) 12 NC_007123.6 (13080237..13125946)

    Chromosome 12 - NC_007123.7Genomic Context describing neighboring genes Neighboring gene coiled-coil serine-rich protein 2b Neighboring gene PAT1 homolog 2 Neighboring gene progestin and adipoQ receptor family member IVb Neighboring gene pelota mRNA surveillance and ribosome rescue factor

    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. Notochordal Signals Establish Phylogenetic Identity of the Teleost Spine. Peskin B, et al. Curr Biol, 2020 Jul 20. PMID 32559448, Free PMC Article
    2. Molecular characterization of Calymmin, a novel notochord sheath-associated extracellular matrix protein in the zebrafish embryo. Cerdà J, et al. Dev Dyn, 2002 Jun. PMID 12112472
    3. Dstyk mutation leads to congenital scoliosis-like vertebral malformations in zebrafish via dysregulated mTORC1/TFEB pathway. Sun X, et al. Nat Commun, 2020 Jan 24. PMID 31980602, Free PMC Article
    4. Genetic Screen for Postembryonic Development in the Zebrafish (Danio rerio): Dominant Mutations Affecting Adult Form. Henke K, et al. Genetics, 2017 Oct. PMID 28835471, Free PMC Article
    5. Zebrafish reward mutants reveal novel transcripts mediating the behavioral effects of amphetamine. Webb KJ, et al. Genome Biol, 2009. PMID 19646228, Free PMC Article

    See all (8) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Calymmin is a novel constitutive protein of the ECM compartment associated to the perinotochordal sheath in the zebrafish embryo
      Title: Molecular characterization of Calymmin, a novel notochord sheath-associated extracellular matrix protein in the zebrafish embryo.
    Submit: New GeneRIF Correction

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by ZFIN

    Process Evidence Code Pubs
    acts_upstream_of_or_within embryonic skeletal system development IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in collagen-containing extracellular matrix IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    calymmin

    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_131014.1 → NP_571089.1  calymmin precursor

      See identical proteins and their annotated locations for NP_571089.1

      Status: PROVISIONAL

      Source sequence(s)
      AF102865
      UniProtKB/TrEMBL
      A0A8M1P6P1, Q9PVF5
      Related
      ENSDARP00000072306.4, ENSDART00000077840.6
      Conserved Domains (1) summary
      pfam09606
      Location:363 → 781
      Med15; ARC105 or Med15 subunit of Mediator complex non-fungal

    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_007123.7 Reference GRCz11 Primary Assembly

      Range
      13118545..13164249
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_005156049.4 → XP_005156106.1  calymmin isoform X1

      UniProtKB/TrEMBL
      A0A8M2B2D4
      Conserved Domains (2) summary
      PTZ00395
      Location:101 → 551
      PTZ00395; Sec24-related protein; Provisional
      pfam09770
      Location:700 → 869
      PAT1; Topoisomerase II-associated protein PAT1

    2. XM_021480020.1 → XP_021335695.1  calymmin isoform X4

      UniProtKB/TrEMBL
      A0A8M9QMD0
      Conserved Domains (1) summary
      cl25764
      Location:596 → 800
      PAT1; Topoisomerase II-associated protein PAT1

    3. XM_017358425.2 → XP_017213914.1  calymmin isoform X3

      UniProtKB/TrEMBL
      A0A8M6Z3G3

    4. XM_009306481.3 → XP_009304756.1  calymmin isoform X6

      UniProtKB/TrEMBL
      A0A8M3AY54
      Conserved Domains (1) summary
      pfam09606
      Location:277 → 738
      Med15; ARC105 or Med15 subunit of Mediator complex non-fungal

    5. XM_009306485.3 → XP_009304760.1  calymmin isoform X8

      UniProtKB/TrEMBL
      A0A8M3AY29
      Conserved Domains (1) summary
      pfam09606
      Location:176 → 636
      Med15; ARC105 or Med15 subunit of Mediator complex non-fungal

    6. XM_017358426.2 → XP_017213915.1  calymmin isoform X5

      UniProtKB/TrEMBL
      A0A8M6Z999

    7. XM_009306483.3 → XP_009304758.1  calymmin isoform X7

      UniProtKB/TrEMBL
      A0A8M3BE10
      Conserved Domains (1) summary
      pfam09606
      Location:227 → 687
      Med15; ARC105 or Med15 subunit of Mediator complex non-fungal

    8. XM_021480021.1 → XP_021335696.1  calymmin isoform X9

      UniProtKB/TrEMBL
      A0A8M9QIJ7
      Conserved Domains (2) summary
      cl25764
      Location:460 → 664
      PAT1; Topoisomerase II-associated protein PAT1
      cl26809
      Location:191 → 364
      Sec23_BS; Sec23/Sec24 beta-sandwich domain

    9. XM_005156050.4 → XP_005156107.1  calymmin isoform X2

      UniProtKB/TrEMBL
      A0A8M2B2X6
      Conserved Domains (2) summary
      PTZ00395
      Location:87 → 537
      PTZ00395; Sec24-related protein; Provisional
      pfam09770
      Location:686 → 855
      PAT1; Topoisomerase II-associated protein PAT1
    Nucleotide Protein Strain
    Heading Accession and Version

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