U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

Links from GEO Profiles

    • Showing Current items.

    rtn1a reticulon 1a [ Danio rerio (zebrafish) ]

    Gene ID: 323706, updated on 2-Nov-2024

    Summary

    Go to the top of the page Help
    Official Symbol
    rtn1aprovided by ZNC
    Official Full Name
    reticulon 1aprovided by ZNC
    Primary source
    ZFIN:ZDB-GENE-030131-2426
    See related
    Ensembl:ENSDARG00000006497 AllianceGenome:ZFIN:ZDB-GENE-030131-2426
    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
    rtn1; rtn5; fb64c01; zgc:73298; zgc:86778; im:7136397; wu:fb64c01; wu:fc07e07; wu:fq24d12; zgc:113566
    Summary
    Predicted to be involved in brain development; endoplasmic reticulum tubular network formation; and neuron differentiation. Predicted to be located in endoplasmic reticulum and membrane. Predicted to be active in endoplasmic reticulum membrane; neuron projection; and postsynaptic density. Is expressed in several structures, including digestive system; nervous system; neural rod; trigeminal placode; and yolk syncytial layer. Orthologous to human RTN1 (reticulon 1). [provided by Alliance of Genome Resources, Nov 2024]
    Orthologs
    human mouse all
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    Go to the top of the page Help
    See rtn1a in Genome Data Viewer
    Location:
    chromosome: 13
    Exon count:
    11
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCz11 (GCF_000002035.6) 13 NC_007124.7 (31424586..31470469, complement)
    105 previous assembly GRCz10 (GCF_000002035.5) 13 NC_007124.6 (31294136..31340019, complement)

    Chromosome 13 - NC_007124.7Genomic Context describing neighboring genes Neighboring gene phosphoglycerate mutase 1a Neighboring gene tudor domain containing 9 Neighboring gene leucine rich repeat containing 9 Neighboring gene pecanex 4

    Genomic regions, transcripts, and products

    Go to the top of the page Help

    Go to nucleotide: Graphics FASTA GenBank

    Expression

    Go to the top of the page Help
    • 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

    Go to the top of the pageHelp

    Related articles in PubMed

    1. Therapeutic potential of N-acetylcysteine in acrylamide acute neurotoxicity in adult zebrafish. Faria M, et al. Sci Rep, 2019 Nov 11. PMID 31712630, Free PMC Article
    2. MYC Drives a Subset of High-Risk Pediatric Neuroblastomas and Is Activated through Mechanisms Including Enhancer Hijacking and Focal Enhancer Amplification. Zimmerman MW, et al. Cancer Discov, 2018 Mar. PMID 29284669, Free PMC Article
    3. Revealing genes associated with vitellogenesis in the liver of the zebrafish (Danio rerio) by transcriptome profiling. Levi L, et al. BMC Genomics, 2009 Mar 31. PMID 19335895, Free PMC Article
    4. Analysis of the reticulon gene family demonstrates the absence of the neurite growth inhibitor Nogo-A in fish. Diekmann H, et al. Mol Biol Evol, 2005 Aug. PMID 15858203
    5. A reticular rhapsody: phylogenic evolution and nomenclature of the RTN/Nogo gene family. Oertle T, et al. FASEB J, 2003 Jul. PMID 12832288

    See all (10) citations in PubMed

    GeneRIFs: Gene References Into Functions

    General gene information

    Go to the top of the page Help

    Markers

    Homology

    Gene Ontology Provided by ZFIN

    Function Evidence Code Pubs
    enables molecular_function ND
    No biological Data available
    more info
    		  
    Process Evidence Code Pubs
    involved_in biological_process ND
    No biological Data available
    more info
    		  
    involved_in brain development IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in endoplasmic reticulum tubular network formation IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in neuron differentiation IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    located_in endoplasmic reticulum IEA
    Inferred from Electronic Annotation
    more info
    		  
    is_active_in endoplasmic reticulum membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in membrane IEA
    Inferred from Electronic Annotation
    more info
    		  
    is_active_in neuron projection IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    is_active_in postsynaptic density IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

    Go to the top of the page Help
    Preferred Names
    reticulon-1a

    NCBI Reference Sequences (RefSeq)

    Go to the top of the page Help

    NEW Try the new Transcript table

    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_001029967.3 → NP_001025138.2  reticulon-1a isoform 1

      See identical proteins and their annotated locations for NP_001025138.2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
      Source sequence(s)
      BX072537
      UniProtKB/TrEMBL
      A0A8M1N713, Q4G5V7
      Related
      ENSDARP00000071046.4, ENSDART00000076574.6
      Conserved Domains (1) summary
      pfam02453
      Location:632 → 796
      Reticulon; Reticulon

    2. NM_001319289.1 → NP_001306218.1  reticulon-1a isoform 3

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) contains an alternate exon in the 5' UTR and 5' coding region, lacks a portion of the 5' coding region, and initiates translation at an alternate start codon, compared to variant 1. The encoded isoform (3) has a distinct N-terminus and is shorter than isoform 1.
      Source sequence(s)
      BX072537, EH487664, EH494741
      UniProtKB/TrEMBL
      A0A8M1P8H2, F1Q8T8
      Related
      ENSDARP00000057440.4, ENSDART00000057441.5
      Conserved Domains (1) summary
      pfam02453
      Location:5 → 169
      Reticulon; Reticulon

    3. NM_199652.2 → NP_955946.1  reticulon-1a isoform 2

      See identical proteins and their annotated locations for NP_955946.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) contains an alternate exon in the 5' UTR and 5' coding region, lacks a portion of the 5' coding region, and initiates translation at an alternate start codon, compared to variant 1. The encoded isoform (2) has a distinct N-terminus and is shorter than isoform 1.
      Source sequence(s)
      BX072537, EH444584, EH594768
      UniProtKB/TrEMBL
      F6NIU5, Q4G5V1, Q6PBQ4
      Related
      ENSDARP00000071042.5, ENSDART00000076571.7
      Conserved Domains (1) summary
      pfam02453
      Location:17 → 181
      Reticulon; Reticulon

    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_007124.7 Reference GRCz11 Primary Assembly

      Range
      31424586..31470469 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein Strain
    Heading Accession and Version

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

    Molecular Biology Databases
    Research Materials
    Tools
    Miscellaneous