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Rtn3 reticulon 3 [ Mus musculus (house mouse) ]

Gene ID: 20168, updated on 8-Feb-2024

Summary

Official Symbol
Rtn3provided by MGI
Official Full Name
reticulon 3provided by MGI
Primary source
MGI:MGI:1339970
See related
Ensembl:ENSMUSG00000024758 AllianceGenome:MGI:1339970
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Mus musculus
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as
RTN3-A1
Summary
Involved in endoplasmic reticulum tubular network formation. Located in synapse. Is expressed in several structures, including genitourinary system; nervous system; olfactory epithelium; retina; and vibrissa. Orthologous to human RTN3 (reticulon 3). [provided by Alliance of Genome Resources, Apr 2022]
Expression
Ubiquitous expression in cortex adult (RPKM 114.3), frontal lobe adult (RPKM 104.4) and 28 other tissues See more
Orthologs
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Genomic context

See Rtn3 in Genome Data Viewer
Location:
19 A; 19 5.32 cM
Exon count:
10
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCm39 (GCF_000001635.27) 19 NC_000085.7 (7403260..7460656, complement)
108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 19 NC_000085.6 (7425895..7483291, complement)

Chromosome 19 - NC_000085.7Genomic Context describing neighboring genes Neighboring gene STARR-seq mESC enhancer starr_45468 Neighboring gene predicted gene, 18842 Neighboring gene microRNA 6991 Neighboring gene zinc finger translocation associated Neighboring gene CapStarr-seq enhancer MGSCv37_chr19:7520209-7520392 Neighboring gene atlastin GTPase 3 Neighboring gene phospholipase A and acyltransferase 3 Neighboring gene STARR-seq mESC enhancer starr_45469 Neighboring gene STARR-seq mESC enhancer starr_45470

Genomic regions, transcripts, and products

Expression

  • Project title: Mouse ENCODE transcriptome data
  • Description: RNA profiling data sets generated by the Mouse ENCODE project.
  • BioProject: PRJNA66167
  • Publication: PMID 25409824
  • Analysis date: n/a

Bibliography

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Variation

Alleles

Alleles of this type are documented at Mouse Genome Informatics  (MGI)
  • Targeted (1)  1 citation
  • Endonuclease-mediated (1) 

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Clone Names

  • MGC105197

Gene Ontology Provided by MGI

Function Evidence Code Pubs
enables protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
Process Evidence Code Pubs
acts_upstream_of_or_within apoptotic process IEA
Inferred from Electronic Annotation
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 endoplasmic reticulum tubular network formation IDA
Inferred from Direct Assay
more info
PubMed 
involved_in endoplasmic reticulum tubular network formation ISO
Inferred from Sequence Orthology
more info
 
involved_in endoplasmic reticulum tubular network organization ISO
Inferred from Sequence Orthology
more info
 
involved_in negative regulation of amyloid-beta formation ISO
Inferred from Sequence Orthology
more info
 
involved_in neuron differentiation IBA
Inferred from Biological aspect of Ancestor
more info
 
acts_upstream_of_or_within vesicle-mediated transport IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
located_in Golgi apparatus ISO
Inferred from Sequence Orthology
more info
 
located_in endoplasmic reticulum ISO
Inferred from Sequence Orthology
more info
 
is_active_in endoplasmic reticulum membrane IBA
Inferred from Biological aspect of Ancestor
more info
 
located_in endoplasmic reticulum membrane ISO
Inferred from Sequence Orthology
more info
 
is_active_in glutamatergic synapse ISO
Inferred from Sequence Orthology
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
 
is_active_in presynapse ISO
Inferred from Sequence Orthology
more info
 
is_active_in synapse EXP
Inferred from Experiment
more info
PubMed 
is_active_in synapse IDA
Inferred from Direct Assay
more info
PubMed 

General protein information

Preferred Names
reticulon-3
Names
Nsp-like II

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_001003933.2NP_001003933.1  reticulon-3 isoform 2

    See identical proteins and their annotated locations for NP_001003933.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2, also known as RTN3-A2) lacks an alternate in-frame exon, compared to variant 1. The encoded isoform (2) is shorter than isoform 1.
    Source sequence(s)
    AC129188, AY427822, BY295849
    Consensus CDS
    CCDS29525.1
    UniProtKB/Swiss-Prot
    Q9ES97
    Related
    ENSMUSP00000085496.5, ENSMUST00000088171.12
    Conserved Domains (1) summary
    pfam02453
    Location:757921
    Reticulon; Reticulon
  2. NM_001003934.2NP_001003934.1  reticulon-3 isoform 1

    See identical proteins and their annotated locations for NP_001003934.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1, also known as Rtn3-A1) represents the longest transcript and encodes the longest isoform (1).
    Source sequence(s)
    AC129188, AY750849, BY295849
    Consensus CDS
    CCDS37906.1
    UniProtKB/Swiss-Prot
    Q3UF62, Q544J1, Q68FE4, Q6IM69, Q6R8K6, Q6R8K7, Q6T929, Q8C6D5, Q8CCU2, Q9ES97
    Related
    ENSMUSP00000065810.6, ENSMUST00000065304.13
    Conserved Domains (1) summary
    pfam02453
    Location:776940
    Reticulon; Reticulon
  3. NM_001271486.1NP_001258415.1  reticulon-3 isoform 5

    See identical proteins and their annotated locations for NP_001258415.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (5) uses an alternate in-frame splice site, compared to variant 1. The encoded isoform (5) is shorter than isoform 1.
    Source sequence(s)
    AC129188, AK032109, AY427822, BY295849
    Consensus CDS
    CCDS89331.1
    UniProtKB/Swiss-Prot
    Q9ES97
    Related
    ENSMUSP00000158024.2, ENSMUST00000235593.2
    Conserved Domains (1) summary
    pfam02453
    Location:455619
    Reticulon; Reticulon
  4. NM_001271487.1NP_001258416.1  reticulon-3 isoform 6

    See identical proteins and their annotated locations for NP_001258416.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (6, also known as RTN3-B2) lacks an alternate in-frame exon, compared to variant 1. The encoded isoform (6) is shorter than isoform 1.
    Source sequence(s)
    AC129188, AY750849, BY295849
    Consensus CDS
    CCDS70927.1
    UniProtKB/Swiss-Prot
    Q9ES97
    Related
    ENSMUSP00000025667.8, ENSMUST00000025667.14
    Conserved Domains (1) summary
    pfam02453
    Location:68232
    Reticulon; Reticulon
  5. NM_053076.3NP_444306.1  reticulon-3 isoform 4

    See identical proteins and their annotated locations for NP_444306.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (4, also known as RTN3-B1) lacks two alternate in-frame exons, compared to variant 1. The encoded isoform (4) is shorter than isoform 1.
    Source sequence(s)
    AC129188, AK036892, BY295849
    Consensus CDS
    CCDS29526.1
    UniProtKB/Swiss-Prot
    Q9ES97
    Related
    ENSMUSP00000085494.7, ENSMUST00000088169.7
    Conserved Domains (1) summary
    pfam02453
    Location:49213
    Reticulon

RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCm39 C57BL/6J

Genomic

  1. NC_000085.7 Reference GRCm39 C57BL/6J

    Range
    7403260..7460656 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017318088.2XP_017173577.1  reticulon-3 isoform X1

    Conserved Domains (1) summary
    pfam02453
    Location:48212
    Reticulon

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NM_001003930.1: Suppressed sequence

    Description
    NM_001003930.1: This RefSeq was permanently suppressed because currently there is insufficient support for the transcript and the protein.