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si:ch73-61d6.3 si:ch73-61d6.3 [ Danio rerio (zebrafish) ]

Gene ID: 100001136, updated on 9-Dec-2024

Summary

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Official Symbol
si:ch73-61d6.3provided by ZNC
Official Full Name
si:ch73-61d6.3provided by ZNC
Primary source
ZFIN:ZDB-GENE-091204-109
See related
Ensembl:ENSDARG00000057826 AllianceGenome:ZFIN:ZDB-GENE-091204-109
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
Summary
Predicted to enable cis-regulatory region sequence-specific DNA binding activity. Predicted to be involved in positive regulation of transcription elongation by RNA polymerase II and snRNA transcription by RNA polymerase II. Predicted to act upstream of or within bicellular tight junction assembly. Predicted to be located in bicellular tight junction and plasma membrane. Predicted to be part of transcription elongation factor complex. [provided by Alliance of Genome Resources, Dec 2024]
Orthologs
all
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Genomic context

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See si:ch73-61d6.3 in Genome Data Viewer
Location:
chromosome: 8
Exon count:
8
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCz11 (GCF_000002035.6) 8 NC_007119.7 (13189962..13220763, complement)
105 previous assembly GRCz10 (GCF_000002035.5) 8 NC_007119.6 (13152385..13183082, complement)

Chromosome 8 - NC_007119.7Genomic Context describing neighboring genes Neighboring gene integrin, beta 4 Neighboring gene zgc:194990 Neighboring gene potassium intermediate/small conductance calcium-activated channel, subfamily N, member 1b Neighboring gene uncharacterized LOC110440006 Neighboring gene uncharacterized LOC101886813 Neighboring gene coiled-coil domain containing 124

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. Evolution of complexity in the zebrafish synapse proteome. Bayés À, et al. Nat Commun, 2017 Mar 2. PMID 28252024, Free PMC Article
  2. RFX transcription factors are essential for hearing in mice. Elkon R, et al. Nat Commun, 2015 Oct 15. PMID 26469318, 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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Homology

Gene Ontology Provided by ZFIN

Process Evidence Code Pubs
acts_upstream_of_or_within bicellular tight junction assembly IEA
Inferred from Electronic Annotation
more info
  
Component Evidence Code Pubs
located_in anchoring junction IEA
Inferred from Electronic Annotation
more info
  
located_in bicellular tight junction IEA
Inferred from Electronic Annotation
more info
  
located_in membrane IEA
Inferred from Electronic Annotation
more info
  
located_in plasma membrane IEA
Inferred from Electronic Annotation
more info
  

General protein information

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Preferred Names
occludin

NCBI Reference Sequences (RefSeq)

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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_007119.7 Reference GRCz11 Primary Assembly

    Range
    13189962..13220763 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_005166908.5 → XP_005166965.1  occludin

    See identical proteins and their annotated locations for XP_005166965.1

    UniProtKB/TrEMBL
    A0A8M1PUX9
    Conserved Domains (3) summary
    pfam01284
    Location:56 → 271
    MARVEL; Membrane-associating domain
    pfam07303
    Location:434 → 529
    Occludin_ELL; Occludin homology domain
    pfam12868
    Location:5 → 61
    DUF3824; Domain of unknwon function (DUF3824)

  2. XM_001341168.8 → XP_001341204.3  occludin

    See identical proteins and their annotated locations for XP_001341204.3

    UniProtKB/TrEMBL
    A0A8M1PUX9
    Related
    ENSDARP00000084974.6, ENSDART00000090541.7
    Conserved Domains (3) summary
    pfam01284
    Location:56 → 271
    MARVEL; Membrane-associating domain
    pfam07303
    Location:434 → 529
    Occludin_ELL; Occludin homology domain
    pfam12868
    Location:5 → 61
    DUF3824; Domain of unknwon function (DUF3824)
Nucleotide Protein
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