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

Summary

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; regulation of postsynapse assembly; and synaptic vesicle clustering. Located in cell body; dendrite; and excitatory synapse. Is active in glutamatergic synapse and postsynaptic density membrane. Orthologous to human SYNDIG1 (synapse differentiation inducing 1). [provided by Alliance of Genome Resources, Nov 2024]
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

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_086021.1 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: 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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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.
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.
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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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)

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

NC_086021.1 Reference GRCr8

Range

158491474..158695174

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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
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
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
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
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
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
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
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
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
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