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    Ntm neurotrimin [ Mus musculus (house mouse) ]

    Gene ID: 235106, updated on 21-Apr-2024

    Summary

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    Official Symbol
    Ntmprovided by MGI
    Official Full Name
    neurotriminprovided by MGI
    Primary source
    MGI:MGI:2446259
    See related
    Ensembl:ENSMUSG00000059974 AllianceGenome:MGI:2446259
    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
    Hnt; Igdcc2; 6230410L23Rik; B230210G24Rik
    Summary
    Predicted to be involved in negative regulation of neuron projection development. Predicted to act upstream of or within cell adhesion. Predicted to be located in several cellular components, including cell surface; excitatory synapse; and perinuclear region of cytoplasm. Is expressed in several structures, including alimentary system; central nervous system; digit mesenchyme; heart; and sensory organ. Orthologous to human NTM (neurotrimin). [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Biased expression in cerebellum adult (RPKM 21.6), frontal lobe adult (RPKM 19.3) and 7 other tissues See more
    Orthologs
    human all
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    Genomic context

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    Location:
    9 A4; 9 14.38 cM
    Exon count:
    13
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCm39 (GCF_000001635.27) 9 NC_000075.7 (28906045..29874565, complement)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 9 NC_000075.6 (28994749..29963269, complement)

    Chromosome 9 - NC_000075.7Genomic Context describing neighboring genes Neighboring gene opioid binding protein/cell adhesion molecule-like Neighboring gene STARR-seq mESC enhancer starr_23633 Neighboring gene predicted gene, 33456 Neighboring gene STARR-seq mESC enhancer starr_23635 Neighboring gene predicted gene, 39313 Neighboring gene STARR-seq mESC enhancer starr_23636 Neighboring gene STARR-seq mESC enhancer starr_23637 Neighboring gene STARR-seq mESC enhancer starr_23639 Neighboring gene STARR-seq mESC enhancer starr_23640 Neighboring gene STARR-seq mESC enhancer starr_23641 Neighboring gene STARR-seq mESC enhancer starr_23644 Neighboring gene STARR-seq mESC enhancer starr_23645 Neighboring gene STARR-seq mESC enhancer starr_23646 Neighboring gene STARR-seq mESC enhancer starr_23647 Neighboring gene predicted gene 15520 Neighboring gene STARR-seq mESC enhancer starr_23648 Neighboring gene STARR-seq mESC enhancer starr_23649 Neighboring gene STARR-seq mESC enhancer starr_23651 Neighboring gene STARR-seq mESC enhancer starr_23652 Neighboring gene STARR-seq mESC enhancer starr_23653 Neighboring gene STARR-seq mESC enhancer starr_23654 Neighboring gene STARR-seq mESC enhancer starr_23656 Neighboring gene predicted gene 15521 Neighboring gene STARR-seq mESC enhancer starr_23657 Neighboring gene STARR-seq mESC enhancer starr_23659 Neighboring gene STARR-seq mESC enhancer starr_23660 Neighboring gene STARR-seq mESC enhancer starr_23661 Neighboring gene predicted gene, 57552 Neighboring gene predicted gene, 19640

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • 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

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    Related articles in PubMed

    1. Deficit in emotional learning in neurotrimin knockout mice. Mazitov T, et al. Behav Brain Res, 2017 Jan 15. PMID 27693610
    2. The combined impact of IgLON family proteins Lsamp and Neurotrimin on developing neurons and behavioral profiles in mouse. Singh K, et al. Brain Res Bull, 2018 Jun. PMID 29605488
    3. Promoter-Specific Expression and Genomic Structure of IgLON Family Genes in Mouse. Vanaveski T, et al. Front Neurosci, 2017. PMID 28210208, Free PMC Article
    4. Gene-targeted deletion of OPCML and Neurotrimin in mice does not yield congenital heart defects. Ye M, et al. Am J Med Genet A, 2014 Apr. PMID 24616287
    5. Spatiotemporal expression of IgLON family members in the developing mouse nervous system. Fearnley S, et al. Sci Rep, 2021 Oct 1. PMID 34599206, Free PMC Article

    See all (35) citations in PubMed

    GeneRIFs: Gene References Into Functions

    Variation

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    Alleles

    Alleles of this type are documented at Mouse Genome Informatics  (MGI)
    • Targeted (3)  1 citation
    • Endonuclease-mediated (3) 

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by MGI

    Process Evidence Code Pubs
    acts_upstream_of_or_within cell adhesion IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in negative regulation of neuron projection development ISO
    Inferred from Sequence Orthology
    more info
    		  
    Component Evidence Code Pubs
    located_in axon ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in cell surface ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in excitatory synapse ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in extracellular space ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in membrane IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in perinuclear region of cytoplasm ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in plasma membrane IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in side of membrane IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    neurotrimin

    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_001357593.1 → NP_001344522.1  neurotrimin isoform 1 precursor

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) encodes the longest isoform (1).
      Source sequence(s)
      AC154494, AC154850, AC155928, AC162927
      UniProtKB/TrEMBL
      Q3TYC2
      Conserved Domains (3) summary
      pfam13927
      Location:222 → 299
      Ig_3; Immunoglobulin domain
      cd00096
      Location:223 → 229
      Ig; putative Ig strand A [structural motif]
      cl11960
      Location:44 → 132
      Ig; Immunoglobulin domain

    2. NM_001357597.1 → NP_001344526.1  neurotrimin isoform 2 precursor

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) lacks an alternate in-frame exon compared to variant 1. The resulting isoform (2) has the same N- and C-termini but is shorter compared to isoform 1.
      Source sequence(s)
      AC154494, AC154850, AC155928, AC162927
      UniProtKB/TrEMBL
      Q3TYC2
      Conserved Domains (3) summary
      smart00409
      Location:233 → 310
      IG; Immunoglobulin
      pfam13927
      Location:136 → 205
      Ig_3; Immunoglobulin domain
      cl11960
      Location:44 → 132
      Ig; Immunoglobulin domain

    3. NM_001357598.1 → NP_001344527.1  neurotrimin isoform 3 precursor

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) lacks an alternate in-frame exon compared to variant 1. The resulting isoform (3) has the same N- and C-termini but is shorter compared to isoform 1.
      Source sequence(s)
      AC154494, AC154850, AC155928, AC162927
      UniProtKB/TrEMBL
      Q3TYC2
      Conserved Domains (3) summary
      pfam13927
      Location:222 → 299
      Ig_3; Immunoglobulin domain
      cd00096
      Location:223 → 229
      Ig; putative Ig strand A [structural motif]
      cl11960
      Location:44 → 132
      Ig; Immunoglobulin domain

    4. NM_001357601.1 → NP_001344530.1  neurotrimin isoform 5 precursor

      Status: VALIDATED

      Description
      Transcript Variant: This variant (5) differs in the 5' UTR and coding sequence and lacks an alternate in-frame exon compared to variant 1. The resulting isoform (5) has a distinct N-terminus and lacks an alternate internal segment compared to isoform 1.
      Source sequence(s)
      AC154494, AC155928, AC162927
      UniProtKB/TrEMBL
      Q3TYC2
      Conserved Domains (3) summary
      smart00410
      Location:233 → 310
      IG_like; Immunoglobulin like
      pfam13927
      Location:136 → 205
      Ig_3; Immunoglobulin domain
      cl11960
      Location:44 → 132
      Ig; Immunoglobulin domain

    5. NM_001357602.1 → NP_001344531.1  neurotrimin isoform 6 precursor

      Status: VALIDATED

      Description
      Transcript Variant: This variant (6) differs in the 5' UTR and coding sequence and lacks two alternate in-frame exons compared to variant 1. The resulting isoform (6) has a distinct N-terminus and lacks an alternate internal segment compared to isoform 1.
      Source sequence(s)
      AC154494, AC155928, AC162927
      Consensus CDS
      CCDS90526.1
      UniProtKB/Swiss-Prot
      Q99PJ0
      UniProtKB/TrEMBL
      Q3TYC2
      Related
      ENSMUSP00000110892.2, ENSMUST00000115237.8
      Conserved Domains (3) summary
      smart00410
      Location:233 → 310
      IG_like; Immunoglobulin like
      pfam13927
      Location:136 → 205
      Ig_3; Immunoglobulin domain
      cl11960
      Location:44 → 132
      Ig; Immunoglobulin domain

    6. NM_001357603.1 → NP_001344532.1  neurotrimin isoform 7

      Status: VALIDATED

      Description
      Transcript Variant: This variant (7) differs in the 5' UTR and coding sequence and lacks two alternate in-frame exons compared to variant 1. The resulting isoform (7) has a shorter and distinct N-terminus and lacks an alternate internal segment compared to isoform 1.
      Source sequence(s)
      AC154494, AC155928, AC162927
      UniProtKB/TrEMBL
      Q3TYC2
      Conserved Domains (3) summary
      smart00409
      Location:209 → 286
      IG; Immunoglobulin
      pfam13927
      Location:112 → 181
      Ig_3; Immunoglobulin domain
      cl11960
      Location:20 → 108
      Ig; Immunoglobulin domain

    7. NM_172290.4 → NP_758494.2  neurotrimin isoform 4 precursor

      See identical proteins and their annotated locations for NP_758494.2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (4) lacks two alternate in-frame exons compared to variant 1. The resulting isoform (4) has the same N- and C-termini but is shorter compared to isoform 1.
      Source sequence(s)
      AC154494, AC154850, AK045973
      Consensus CDS
      CCDS22943.1
      UniProtKB/TrEMBL
      Q3TYC2, Q8BG33
      Related
      ENSMUSP00000074578.5, ENSMUST00000075069.11
      Conserved Domains (3) summary
      pfam13927
      Location:222 → 299
      Ig_3; Immunoglobulin domain
      cd00096
      Location:223 → 229
      Ig; putative Ig strand A [structural motif]
      cl11960
      Location:44 → 132
      Ig; Immunoglobulin domain

    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_000075.7 Reference GRCm39 C57BL/6J

      Range
      28906045..29874565 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_036154867.1 → XP_036010760.1  neurotrimin isoform X5

      UniProtKB/TrEMBL
      Q3TYC2
      Conserved Domains (3) summary
      pfam13927
      Location:181 → 258
      Ig_3; Immunoglobulin domain
      cd00096
      Location:182 → 188
      Ig; putative Ig strand A [structural motif]
      cl11960
      Location:3 → 91
      Ig; Immunoglobulin domain

    2. XM_036154866.1 → XP_036010759.1  neurotrimin isoform X4

      UniProtKB/TrEMBL
      Q3TYC2
      Conserved Domains (3) summary
      pfam13927
      Location:95 → 164
      Ig_3; Immunoglobulin domain
      cd00096
      Location:182 → 188
      Ig; putative Ig strand A [structural motif]
      cl11960
      Location:182 → 266
      Ig; Immunoglobulin domain

    3. XM_036154865.1 → XP_036010758.1  neurotrimin isoform X3

      UniProtKB/TrEMBL
      Q3TYC2
      Conserved Domains (3) summary
      pfam13927
      Location:181 → 258
      Ig_3; Immunoglobulin domain
      cd00096
      Location:182 → 188
      Ig; putative Ig strand A [structural motif]
      cl11960
      Location:3 → 91
      Ig; Immunoglobulin domain

    4. XM_006510209.5 → XP_006510272.1  neurotrimin isoform X1

      UniProtKB/TrEMBL
      Q3TYC2
      Conserved Domains (3) summary
      smart00408
      Location:125 → 181
      IGc2; Immunoglobulin C-2 Type
      smart00409
      Location:209 → 286
      IG; Immunoglobulin
      cl11960
      Location:20 → 108
      Ig; Immunoglobulin domain

    5. XM_036154864.1 → XP_036010757.1  neurotrimin isoform X2

      UniProtKB/TrEMBL
      Q3TYC2
      Conserved Domains (3) summary
      pfam13927
      Location:198 → 275
      Ig_3; Immunoglobulin domain
      cd00096
      Location:199 → 205
      Ig; putative Ig strand A [structural motif]
      cl11960
      Location:20 → 108
      Ig; Immunoglobulin domain

    6. XM_006510211.5 → XP_006510274.1  neurotrimin isoform X6

      UniProtKB/TrEMBL
      F6RQ26
      Related
      ENSMUSP00000119030.2, ENSMUST00000155308.8
      Conserved Domains (2) summary
      smart00410
      Location:96 → 173
      IG_like; Immunoglobulin like
      cl11960
      Location:42 → 68
      Ig; Immunoglobulin domain
    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q99PJ0.2 GenPept UniProtKB/Swiss-Prot:Q99PJ0

    Gene LinkOut

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