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rtn1a reticulon 1a [ Danio rerio (zebrafish) ]

Gene ID: 323706, updated on 12-Sep-2024

Summary

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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 located in endoplasmic reticulum membrane. Predicted to be integral component of membrane. 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, Apr 2022]
Orthologs
human mouse all
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Genomic context

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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

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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 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. 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

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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

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Preferred Names
reticulon-1a

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_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

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