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    zgc:65895 zgc:65895 [ Danio rerio (zebrafish) ]

    Gene ID: 393546, updated on 9-Dec-2024

    Summary

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    Official Symbol
    zgc:65895provided by ZNC
    Official Full Name
    zgc:65895provided by ZNC
    Primary source
    ZFIN:ZDB-GENE-040426-1466
    See related
    Ensembl:ENSDARG00000034086 AllianceGenome:ZFIN:ZDB-GENE-040426-1466
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Danio rerio
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes; Danionidae; Danioninae; Danio
    Also known as
    TGFB1I4; zgc:77475
    Summary
    Predicted to act upstream of or within regulation of transcription by RNA polymerase II. Predicted to be located in cytoplasm and nucleus. [provided by Alliance of Genome Resources, Dec 2024]
    Annotation information
    Annotation category: partial on reference assembly
    Note: NM_200574.4 may not be a complete representation of the structure of GeneID 393546 due to the incomplete nature of the assembly in this region of the genome. [24 Oct 2014]
    Orthologs
    all
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    Genomic context

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    See zgc:65895 in Genome Data Viewer
    Location:
    chromosome: 6
    Exon count:
    4
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCz11 (GCF_000002035.6) 6 NC_007117.7 (59967994..59973132)
    105 previous assembly GRCz10 (GCF_000002035.5) 6 NC_007117.6 (59760528..59767906)

    Chromosome 6 - NC_007117.7Genomic Context describing neighboring genes Neighboring gene G-protein coupled bile acid receptor 1 Neighboring gene nuclear FMR1 interacting protein 1 Neighboring gene F-box and leucine-rich repeat protein 3b Neighboring gene coiled-coil domain containing 122 Neighboring gene mitochondrial translational release factor 1

    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. RFX transcription factors are essential for hearing in mice. Elkon R, et al. Nat Commun, 2015 Oct 15. PMID 26469318, Free PMC Article
    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

    • MGC65895

    Gene Ontology Provided by ZFIN

    Process Evidence Code Pubs
    acts_upstream_of_or_within regulation of transcription by RNA polymerase II IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    located_in cytoplasm IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in nucleus IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    uncharacterized protein LOC393546
    Names
    transforming growth factor beta 1 induced transcript 4

    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_200574.4 → NP_956868.1  uncharacterized protein LOC393546

      See identical proteins and their annotated locations for NP_956868.1

      Status: VALIDATED

      Source sequence(s)
      CABZ01075209, CABZ01075210, FP219083
      UniProtKB/TrEMBL
      Q6NZS2, Q6PHC8
      Related
      ENSDARP00000050456.5, ENSDART00000050457.7
      Conserved Domains (1) summary
      pfam01166
      Location:55 → 101
      TSC22; TSC-22/dip/bun family

    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_007117.7 Reference GRCz11 Primary Assembly

      Range
      59967994..59973132
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_017356454.3 → XP_017211943.1  uncharacterized protein LOC393546 isoform X1

      UniProtKB/TrEMBL
      Q6NZS2, Q6PHC8
      Conserved Domains (1) summary
      pfam01166
      Location:55 → 101
      TSC22; TSC-22/dip/bun family
    Nucleotide Protein Strain
    Heading Accession and Version

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