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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

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