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    Igsf9 immunoglobulin superfamily, member 9 [ Rattus norvegicus (Norway rat) ]

    Gene ID: 304982, updated on 2-Nov-2024

    Summary

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    Official Symbol
    Igsf9provided by RGD
    Official Full Name
    immunoglobulin superfamily, member 9provided by RGD
    Primary source
    RGD:1304566
    See related
    EnsemblRapid:ENSRNOG00000008054 AllianceGenome:RGD:1304566
    Gene type
    protein coding
    RefSeq status
    PROVISIONAL
    Organism
    Rattus norvegicus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
    Summary
    Predicted to enable cell-cell adhesion mediator activity. Involved in regulation of synapse maturation. Is active in glutamatergic synapse and postsynaptic density membrane. Orthologous to human IGSF9 (immunoglobulin superfamily member 9). [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Biased expression in Kidney (RPKM 30.4), Uterus (RPKM 13.9) and 9 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    See Igsf9 in Genome Data Viewer
    Location:
    13q24
    Exon count:
    23
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 13 NC_086031.1 (87480979..87497974)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 13 NC_051348.1 (84948643..84965616)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 13 NC_005112.4 (90809459..90832300, complement)

    Chromosome 13 - NC_086031.1Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC108353436 Neighboring gene SLAM family member 9 Neighboring gene transgelin 2 Neighboring gene uncharacterized LOC134481593

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
    • Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
    • BioProject: PRJNA238328
    • Publication: PMID 24510058
    • Analysis date: Mon Jun 6 17:44:12 2016

    Bibliography

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    Related articles in PubMed

    1. The immunoglobulin family member dendrite arborization and synapse maturation 1 (Dasm1) controls excitatory synapse maturation. Shi SH, et al. Proc Natl Acad Sci U S A, 2004 Sep 7. PMID 15340156, Free PMC Article
    2. Control of dendrite arborization by an Ig family member, dendrite arborization and synapse maturation 1 (Dasm1). Shi SH, et al. Proc Natl Acad Sci U S A, 2004 Sep 7. PMID 15340157, Free PMC Article
    3. Genetic evidence for the adhesion protein IgSF9/Dasm1 to regulate inhibitory synapse development independent of its intracellular domain. Mishra A, et al. J Neurosci, 2014 Mar 19. PMID 24647940, Free PMC Article
    4. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, et al. Brief Bioinform, 2011 Sep. PMID 21873635, Free PMC Article

    GeneRIFs: Gene References Into Functions

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by RGD

    Function Evidence Code Pubs
    enables cell-cell adhesion mediator activity ISO
    Inferred from Sequence Orthology
    more info
    		  
    Process Evidence Code Pubs
    acts_upstream_of_or_within dendrite development ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within homophilic cell adhesion via plasma membrane adhesion molecules ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in regulation of synapse maturation IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in regulation of synapse maturation IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within regulation of synapse organization ISO
    Inferred from Sequence Orthology
    more info
    		  
    Component Evidence Code Pubs
    located_in axon ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in dendrite ISO
    Inferred from Sequence Orthology
    more info
    		  
    is_active_in glutamatergic synapse IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    is_active_in glutamatergic synapse IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    located_in inhibitory 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 membrane IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    protein turtle homolog A
    Names
    dendrite arborization and synapse maturation protein 1
    igSF9A
    immunoglobulin superfamily member 9A

    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_001107197.1 → NP_001100667.1  protein turtle homolog A precursor

      See identical proteins and their annotated locations for NP_001100667.1

      Status: PROVISIONAL

      Source sequence(s)
      CH473985
      UniProtKB/Swiss-Prot
      P0C5H6
      Related
      ENSRNOP00000010930.5, ENSRNOT00000010930.9
      Conserved Domains (7) summary
      smart00409
      Location:28 → 110
      IG; Immunoglobulin
      smart00410
      Location:143 → 223
      IG_like; Immunoglobulin like
      PHA03247
      Location:777 → 1062
      PHA03247; large tegument protein UL36; Provisional
      cd00063
      Location:625 → 715
      FN3; Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all ...
      pfam13927
      Location:226 → 305
      Ig_3; Immunoglobulin domain
      cd00096
      Location:136 → 139
      Ig; Ig strand A [structural motif]
      cl11960
      Location:418 → 503
      Ig; Immunoglobulin domain

    RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

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

    Reference GRCr8

    Genomic

    1. NC_086031.1 Reference GRCr8

      Range
      87480979..87497974
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006250290.5 → XP_006250352.1  protein turtle homolog A isoform X1

      See identical proteins and their annotated locations for XP_006250352.1

      UniProtKB/Swiss-Prot
      P0C5H6
      Conserved Domains (7) summary
      smart00409
      Location:28 → 110
      IG; Immunoglobulin
      smart00410
      Location:143 → 223
      IG_like; Immunoglobulin like
      PHA03247
      Location:777 → 1062
      PHA03247; large tegument protein UL36; Provisional
      cd00063
      Location:625 → 715
      FN3; Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all ...
      pfam13927
      Location:226 → 305
      Ig_3; Immunoglobulin domain
      cd00096
      Location:136 → 139
      Ig; Ig strand A [structural motif]
      cl11960
      Location:418 → 503
      Ig; Immunoglobulin domain

    2. XM_063272374.1 → XP_063128444.1  protein turtle homolog A isoform X4

    3. XM_063272373.1 → XP_063128443.1  protein turtle homolog A isoform X3

    4. XM_039090799.2 → XP_038946727.1  protein turtle homolog A isoform X2

      UniProtKB/TrEMBL
      A0A8L2R0J7
      Related
      ENSRNOP00000069173.2, ENSRNOT00000086508.3
      Conserved Domains (6) summary
      smart00409
      Location:80 → 160
      IG; Immunoglobulin
      PHA03247
      Location:714 → 999
      PHA03247; large tegument protein UL36; Provisional
      cd00063
      Location:562 → 652
      FN3; Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all ...
      pfam13927
      Location:163 → 242
      Ig_3; Immunoglobulin domain
      cd00096
      Location:163 → 167
      Ig; putative Ig strand A [structural motif]
      cl11960
      Location:355 → 440
      Ig; Immunoglobulin domain

    5. XM_039090798.1 → XP_038946726.1  protein turtle homolog A isoform X1

      UniProtKB/Swiss-Prot
      P0C5H6
      Conserved Domains (7) summary
      smart00409
      Location:28 → 110
      IG; Immunoglobulin
      smart00410
      Location:143 → 223
      IG_like; Immunoglobulin like
      PHA03247
      Location:777 → 1062
      PHA03247; large tegument protein UL36; Provisional
      cd00063
      Location:625 → 715
      FN3; Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all ...
      pfam13927
      Location:226 → 305
      Ig_3; Immunoglobulin domain
      cd00096
      Location:136 → 139
      Ig; Ig strand A [structural motif]
      cl11960
      Location:418 → 503
      Ig; Immunoglobulin domain

    6. XM_039090797.2 → XP_038946725.1  protein turtle homolog A isoform X1

      UniProtKB/Swiss-Prot
      P0C5H6
      Conserved Domains (7) summary
      smart00409
      Location:28 → 110
      IG; Immunoglobulin
      smart00410
      Location:143 → 223
      IG_like; Immunoglobulin like
      PHA03247
      Location:777 → 1062
      PHA03247; large tegument protein UL36; Provisional
      cd00063
      Location:625 → 715
      FN3; Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all ...
      pfam13927
      Location:226 → 305
      Ig_3; Immunoglobulin domain
      cd00096
      Location:136 → 139
      Ig; Ig strand A [structural motif]
      cl11960
      Location:418 → 503
      Ig; Immunoglobulin domain
    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    P0C5H6.1 GenPept UniProtKB/Swiss-Prot:P0C5H6

    Gene LinkOut

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

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