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Syndig1 synapse differentiation inducing 1 [ Rattus norvegicus (Norway rat) ]

Gene ID: 362235, updated on 17-Aug-2024

Summary

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Symbol
Syndig1provided by RGD
Full Name
synapse differentiation inducing 1provided by RGD
Primary source
RGD:1310753
See related
EnsemblRapid:ENSRNOG00000031536 AllianceGenome:RGD:1310753
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
Also known as
DSPC2; Tmem90b; RGD1310753
Summary
Predicted to enable glutamate receptor binding activity and protein homodimerization activity. Involved in positive regulation of synapse assembly and synaptic vesicle clustering. Located in cell body; dendrite; and excitatory synapse. Orthologous to human SYNDIG1 (synapse differentiation inducing 1). [provided by Alliance of Genome Resources, Apr 2022]
Expression
Biased expression in Brain (RPKM 161.7), Heart (RPKM 19.1) and 5 other tissues See more
Orthologs
human mouse all
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Genomic context

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See Syndig1 in Genome Data Viewer
Location:
3q41
Exon count:
10
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCr8 (GCF_036323735.1) 3 NC_086021.1 (158491474..158695174)
RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 3 NC_051338.1 (138030995..138234646)
106 previous assembly Rnor_6.0 (GCF_000001895.5) 3 NC_005102.4 (145031427..145199273)

Chromosome 3 - NC_086021.1Genomic Context describing neighboring genes Neighboring gene cystatin D Neighboring gene uncharacterized LOC134486463 Neighboring gene uncharacterized LOC102551848 Neighboring gene uncharacterized LOC120101729 Neighboring gene magnesium transporter NIPA1-like Neighboring gene calcineurin subunit B type 1-like Neighboring gene protein SET-like

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. SynDIG1 promotes excitatory synaptogenesis independent of AMPA receptor trafficking and biophysical regulation. Lovero KL, et al. PLoS One, 2013. PMID 23785483, Free PMC Article
  2. SynDIG1 regulation of excitatory synapse maturation. Díaz E. J Physiol, 2012 Jan 1. PMID 21878521, Free PMC Article
  3. SynDIG1: an activity-regulated, AMPA- receptor-interacting transmembrane protein that regulates excitatory synapse development. Kalashnikova E, et al. Neuron, 2010 Jan 14. PMID 20152115, Free PMC Article
  4. SynDIG4/Prrt1 Is Required for Excitatory Synapse Development and Plasticity Underlying Cognitive Function. Matt L, et al. Cell Rep, 2018 Feb 27. PMID 29490264, Free PMC Article
  5. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). Gerhard DS, et al. Genome Res, 2004 Oct. PMID 15489334, Free PMC Article

See all (7) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. SynDIG1 is not a typical auxiliary subunit to AMPA receptors, but instead is a protein critical to excitatory synaptogenesis.
    Title: SynDIG1 promotes excitatory synaptogenesis independent of AMPA receptor trafficking and biophysical regulation.
  2. An interesting aspect of SynDIG1 is that its distribution at excitatory synapses is regulated by activity, suggesting that SynDIG1 might also play a role in synaptic plasticity.
    Title: SynDIG1 regulation of excitatory synapse maturation.
  3. Results describe SynDIG1 as an activity-regulated transmembrane protein that regulates AMPA receptor content and excitatory synapse development.
    Title: SynDIG1: an activity-regulated, AMPA- receptor-interacting transmembrane protein that regulates excitatory synapse development.
Submit: New GeneRIF Correction

General gene information

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Homology

Gene Ontology Provided by RGD

Function Evidence Code Pubs
enables glutamate receptor binding ISO
Inferred from Sequence Orthology
more info
  
enables glutamate receptor binding ISS
Inferred from Sequence or Structural Similarity
more info
  
enables protein homodimerization activity ISO
Inferred from Sequence Orthology
more info
  
enables protein homodimerization activity ISS
Inferred from Sequence or Structural Similarity
more info
  
Process Evidence Code Pubs
involved_in biological_process ND
No biological Data available
more info
  
involved_in intracellular protein transport ISO
Inferred from Sequence Orthology
more info
  
involved_in intracellular protein transport ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in positive regulation of synapse assembly IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in positive regulation of synapse assembly IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in positive regulation of synapse assembly ISO
Inferred from Sequence Orthology
more info
  
involved_in regulation of postsynapse assembly EXP
Inferred from Experiment
more info
 PubMed 
involved_in regulation of postsynapse assembly IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in regulation of postsynapse assembly IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in synaptic vesicle clustering IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in synaptic vesicle clustering IDA
Inferred from Direct Assay
more info
 PubMed 
Component Evidence Code Pubs
NOT located_in Golgi membrane ISO
Inferred from Sequence Orthology
more info
  
located_in cell body IDA
Inferred from Direct Assay
more info
 PubMed 
located_in dendritic shaft IDA
Inferred from Direct Assay
more info
 PubMed 
located_in dendritic spine IDA
Inferred from Direct Assay
more info
 PubMed 
located_in early endosome membrane ISO
Inferred from Sequence Orthology
more info
  
located_in early endosome membrane ISS
Inferred from Sequence or Structural Similarity
more info
  
is_active_in excitatory synapse IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in excitatory synapse IDA
Inferred from Direct Assay
more info
 PubMed 
is_active_in glutamatergic synapse EXP
Inferred from Experiment
more info
 PubMed 
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 
is_active_in intracellular membrane-bounded organelle IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in intracellular membrane-bounded organelle ISO
Inferred from Sequence Orthology
more info
  
located_in plasma membrane ISO
Inferred from Sequence Orthology
more info
  
located_in plasma membrane ISS
Inferred from Sequence or Structural Similarity
more info
  
located_in postsynaptic density ISO
Inferred from Sequence Orthology
more info
  
located_in postsynaptic density ISS
Inferred from Sequence or Structural Similarity
more info
  
is_active_in postsynaptic density membrane IBA
Inferred from Biological aspect of Ancestor
more info
  
is_active_in postsynaptic density membrane IDA
Inferred from Direct Assay
more info
 PubMed 
located_in postsynaptic density membrane ISO
Inferred from Sequence Orthology
more info
  
is_active_in synaptic vesicle membrane IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in synaptic vesicle membrane ISO
Inferred from Sequence Orthology
more info
  

General protein information

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Preferred Names
synapse differentiation-inducing gene protein 1
Names
dispanin subfamily C member 2
transmembrane protein 90B

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_001025020.1 → NP_001020191.1  synapse differentiation-inducing gene protein 1

    See identical proteins and their annotated locations for NP_001020191.1

    Status: PROVISIONAL

    Source sequence(s)
    BC092131
    UniProtKB/Swiss-Prot
    Q58DZ9
    UniProtKB/TrEMBL
    A6K7G0
    Related
    ENSRNOP00000060788.2, ENSRNOT00000068210.5
    Conserved Domains (1) summary
    pfam04505
    Location:177 → 242
    CD225; Interferon-induced transmembrane protein

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_086021.1 Reference GRCr8

    Range
    158491474..158695174
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017591918.3 → XP_017447407.1  synapse differentiation-inducing gene protein 1 isoform X1

    UniProtKB/Swiss-Prot
    Q58DZ9
    UniProtKB/TrEMBL
    A6K7G0
    Conserved Domains (1) summary
    pfam04505
    Location:177 → 242
    CD225; Interferon-induced transmembrane protein

  2. XM_039105481.2 → XP_038961409.1  synapse differentiation-inducing gene protein 1 isoform X2

    Conserved Domains (1) summary
    pfam04505
    Location:177 → 206
    CD225; Interferon-induced transmembrane protein

  3. XM_039105477.2 → XP_038961405.1  synapse differentiation-inducing gene protein 1 isoform X1

    UniProtKB/Swiss-Prot
    Q58DZ9
    UniProtKB/TrEMBL
    A6K7G0
    Conserved Domains (1) summary
    pfam04505
    Location:177 → 242
    CD225; Interferon-induced transmembrane protein

  4. XM_017591922.3 → XP_017447411.1  synapse differentiation-inducing gene protein 1 isoform X1

    UniProtKB/Swiss-Prot
    Q58DZ9
    UniProtKB/TrEMBL
    A6K7G0
    Conserved Domains (1) summary
    pfam04505
    Location:177 → 242
    CD225; Interferon-induced transmembrane protein

  5. XM_017591916.3 → XP_017447405.1  synapse differentiation-inducing gene protein 1 isoform X1

    UniProtKB/Swiss-Prot
    Q58DZ9
    UniProtKB/TrEMBL
    A6K7G0
    Conserved Domains (1) summary
    pfam04505
    Location:177 → 242
    CD225; Interferon-induced transmembrane protein

  6. XM_039105478.2 → XP_038961406.1  synapse differentiation-inducing gene protein 1 isoform X1

    UniProtKB/Swiss-Prot
    Q58DZ9
    UniProtKB/TrEMBL
    A6K7G0
    Conserved Domains (1) summary
    pfam04505
    Location:177 → 242
    CD225; Interferon-induced transmembrane protein

  7. XM_039105480.2 → XP_038961408.1  synapse differentiation-inducing gene protein 1 isoform X1

    UniProtKB/Swiss-Prot
    Q58DZ9
    UniProtKB/TrEMBL
    A6K7G0
    Conserved Domains (1) summary
    pfam04505
    Location:177 → 242
    CD225; Interferon-induced transmembrane protein

  8. XM_017591920.3 → XP_017447409.1  synapse differentiation-inducing gene protein 1 isoform X1

    UniProtKB/Swiss-Prot
    Q58DZ9
    UniProtKB/TrEMBL
    A6K7G0
    Conserved Domains (1) summary
    pfam04505
    Location:177 → 242
    CD225; Interferon-induced transmembrane protein

  9. XM_017591912.3 → XP_017447401.1  synapse differentiation-inducing gene protein 1 isoform X1

    UniProtKB/Swiss-Prot
    Q58DZ9
    UniProtKB/TrEMBL
    A6K7G0
    Conserved Domains (1) summary
    pfam04505
    Location:177 → 242
    CD225; Interferon-induced transmembrane protein

  10. XM_017591913.3 → XP_017447402.1  synapse differentiation-inducing gene protein 1 isoform X1

    UniProtKB/Swiss-Prot
    Q58DZ9
    UniProtKB/TrEMBL
    A6K7G0
    Conserved Domains (1) summary
    pfam04505
    Location:177 → 242
    CD225; Interferon-induced transmembrane protein

RNA

  1. XR_005501940.2 RNA Sequence

Nucleotide Protein Strain
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q58DZ9.1 GenPept UniProtKB/Swiss-Prot:Q58DZ9

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