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Aliases for SYNDIG1 Gene

Aliases for SYNDIG1 Gene

  • Synapse Differentiation Inducing 1 2 3
  • Transmembrane Protein 90B 2 3 4
  • TMEM90B 3 4 6
  • Interferon Induced Transmembrane Protein Domain Containing 5 2 3
  • Synapse Differentiation Induced Gene 1 2 3
  • Dispanin Subfamily C Member 2 3 4
  • C20orf39 3 4
  • DSPC2 3 4
  • Synapse Differentiation-Inducing Gene Protein 1 3
  • Chromosome 20 Open Reading Frame 39 2
  • IFITMD5 3
  • SynDIG1 4

External Ids for SYNDIG1 Gene

Previous HGNC Symbols for SYNDIG1 Gene

  • C20orf39
  • TMEM90B

Summaries for SYNDIG1 Gene

Entrez Gene Summary for SYNDIG1 Gene

  • This gene encodes a protein that belongs to the interferon-induced transmembrane family of proteins. A similar protein in rat is thought to regulate the development of excitatory synapses. [provided by RefSeq, Jul 2013]

GeneCards Summary for SYNDIG1 Gene

SYNDIG1 (Synapse Differentiation Inducing 1) is a Protein Coding gene. GO annotations related to this gene include protein homodimerization activity and glutamate receptor binding. An important paralog of this gene is TMEM91.

UniProtKB/Swiss-Prot for SYNDIG1 Gene

  • May regulate AMPA receptor content at nascent synapses, and have a role in postsynaptic development and maturation.

No data available for Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for SYNDIG1 Gene

Genomics for SYNDIG1 Gene

Epigenetics Products

  • DNA Methylation CpG Assay Predesigned for Pyrosequencing in human,mouse,rat

Genomic Location for SYNDIG1 Gene

24,469,199 bp from pter
24,666,617 bp from pter
197,419 bases
Plus strand

Genomic View for SYNDIG1 Gene

UCSC Golden Path with GeneCards custom track
Cytogenetic band:
Genomic Location for SYNDIG1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for SYNDIG1 Gene

No data available for Regulatory Elements for SYNDIG1 Gene

Proteins for SYNDIG1 Gene

  • Protein details for SYNDIG1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Synapse differentiation-inducing gene protein 1
    Protein Accession:
    Secondary Accessions:
    • Q6IA30
    • Q9H514

    Protein attributes for SYNDIG1 Gene

    258 amino acids
    Molecular mass:
    28551 Da
    Quaternary structure:
    • Homodimer. Interacts with GRIA1 and GRIA2 (By similarity).

neXtProt entry for SYNDIG1 Gene

Proteomics data for SYNDIG1 Gene at MOPED

Post-translational modifications for SYNDIG1 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for SYNDIG1 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for SYNDIG1 Gene

Domains for SYNDIG1 Gene

Protein Domains for SYNDIG1 Gene


Graphical View of Domain Structure for InterPro Entry



  • Q9H7V2
  • Belongs to the CD225/Dispanin family.
genes like me logo Genes that share domains with SYNDIG1: view

No data available for Gene Families and Suggested Antigen Peptide Sequences for SYNDIG1 Gene

Function for SYNDIG1 Gene

Molecular function for SYNDIG1 Gene

UniProtKB/Swiss-Prot Function: May regulate AMPA receptor content at nascent synapses, and have a role in postsynaptic development and maturation.

Gene Ontology (GO) - Molecular Function for SYNDIG1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 25416956
GO:0035254 glutamate receptor binding ISS --
GO:0042803 protein homodimerization activity ISS --
genes like me logo Genes that share ontologies with SYNDIG1: view

Animal Model Products

CRISPR Products

miRNA for SYNDIG1 Gene

miRTarBase miRNAs that target SYNDIG1

Inhibitory RNA Products

  • Predesigned siRNA for gene silencing in human,mouse,rat for SYNDIG1

In Situ Assay Products

Flow Cytometry Products

No data available for Enzyme Numbers (IUBMB) , Phenotypes , Animal Models , Transcription Factor Targeting and HOMER Transcription for SYNDIG1 Gene

Localization for SYNDIG1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for SYNDIG1 Gene

Cell membrane; Single-pass type II membrane protein. Early endosome membrane; Single-pass type II membrane protein. Cell junction, synapse, postsynaptic cell membrane, postsynaptic density. Cell junction, synapse. Cell projection, dendrite. Cell projection, dendritic spine. Note=Shuttles between the cell surface and early endosome membrane. {ECO:0000250}.

Gene Ontology (GO) - Cellular Components for SYNDIG1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005887 integral component of plasma membrane ISS --
GO:0014069 postsynaptic density ISS --
GO:0016021 integral component of membrane --
GO:0030054 cell junction IEA --
GO:0031901 early endosome membrane ISS --
genes like me logo Genes that share ontologies with SYNDIG1: view

No data available for Subcellular locations from COMPARTMENTS for SYNDIG1 Gene

Pathways for SYNDIG1 Gene

SuperPathways for SYNDIG1 Gene

No Data Available

Interacting Proteins for SYNDIG1 Gene

STRING Interaction Network Preview (showing 1 interactants - click image to see details)
Selected Interacting proteins: Q9H7V2-SYNG1_HUMAN ENSP00000366058 for SYNDIG1 Gene via MINT STRING UniProtKB I2D

Gene Ontology (GO) - Biological Process for SYNDIG1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006886 intracellular protein transport ISS --
GO:0009607 response to biotic stimulus IEA --
GO:0051965 positive regulation of synapse assembly IDA 20152115
GO:0097091 synaptic vesicle clustering ISS --
genes like me logo Genes that share ontologies with SYNDIG1: view

No data available for Pathways by source for SYNDIG1 Gene

Transcripts for SYNDIG1 Gene

mRNA/cDNA for SYNDIG1 Gene

Unigene Clusters for SYNDIG1 Gene

Synapse differentiation inducing 1:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

  • Predesigned siRNA for gene silencing in human,mouse,rat for SYNDIG1

Primer Products

  • QuantiTect SYBR Green Assays in human,mouse,rat
  • Pre-validated RT² qPCR Primer Assay in human,mouse,rat
  • QuantiFast Probe-based Assays in human,mouse,rat

Flow Cytometry Products

Alternative Splicing Database (ASD) splice patterns (SP) for SYNDIG1 Gene

No ASD Table

Relevant External Links for SYNDIG1 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for SYNDIG1 Gene

mRNA expression in normal human tissues for SYNDIG1 Gene

mRNA differential expression in normal tissues according to GTEx for SYNDIG1 Gene

This gene is overexpressed in Brain - Spinal cord (cervical c-1) (4.6), Brain - Cortex (4.1), and Brain - Cerebellum (4.0).

Integrated Proteomics: protein expression from ProteomicsDB and MOPED for SYNDIG1 Gene

SOURCE GeneReport for Unigene cluster for SYNDIG1 Gene Hs.124638

genes like me logo Genes that share expressions with SYNDIG1: view

In Situ Assay Products

No data available for mRNA Expression by UniProt/SwissProt for SYNDIG1 Gene

Orthologs for SYNDIG1 Gene

This gene was present in the common ancestor of chordates.

Orthologs for SYNDIG1 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia SYNDIG1 35
  • 99.74 (n)
  • 100 (a)
TMEM90B 36
  • 100 (a)
(Bos Taurus)
Mammalia SYNDIG1 35
  • 85.27 (n)
  • 86.43 (a)
  • 86 (a)
(Canis familiaris)
Mammalia SYNDIG1 36
  • 94 (a)
TMEM90B 35
  • 90.57 (n)
  • 93.8 (a)
(Mus musculus)
Mammalia Syndig1 35
  • 87.73 (n)
  • 93.02 (a)
Syndig1 16
Syndig1 36
  • 93 (a)
(Monodelphis domestica)
Mammalia SYNDIG1 36
  • 98 (a)
(Ornithorhynchus anatinus)
Mammalia SYNDIG1 36
  • 76 (a)
(Rattus norvegicus)
Mammalia Syndig1 35
  • 87.98 (n)
  • 91.47 (a)
(Gallus gallus)
Aves SYNDIG1 35
  • 80.99 (n)
  • 86.33 (a)
  • 86 (a)
(Anolis carolinensis)
Reptilia SYNDIG1 36
  • 77 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia syndig1 35
  • 74.68 (n)
  • 82.56 (a)
(Danio rerio)
Actinopterygii LOC792553 35
  • 73.25 (n)
  • 72.96 (a)
  • 63 (a)
Species with no ortholog for SYNDIG1:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • fruit fly (Drosophila melanogaster)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for SYNDIG1 Gene

Gene Tree for SYNDIG1 (if available)
Gene Tree for SYNDIG1 (if available)

Paralogs for SYNDIG1 Gene

Paralogs for SYNDIG1 Gene

Selected SIMAP similar genes for SYNDIG1 Gene using alignment to 1 proteins:

genes like me logo Genes that share paralogs with SYNDIG1: view

Variants for SYNDIG1 Gene

Sequence variations from dbSNP and Humsavar for SYNDIG1 Gene

SNP ID Clin Chr 20 pos Sequence Context AA Info Type MAF
rs715863 -- 24,545,212(+) CGGGA(A/G)GCCCA intron-variant
rs719491 -- 24,497,300(+) AGTTC(A/G)AGCAA intron-variant
rs727409 -- 24,576,891(+) TTCTC(C/T)ACCTG intron-variant
rs729540 -- 24,663,929(+) ACTGC(C/T)GCATG intron-variant
rs729541 -- 24,664,046(+) GTCCA(C/T)AGTGA intron-variant

Structural Variations from Database of Genomic Variants (DGV) for SYNDIG1 Gene

Variant ID Type Subtype PubMed ID
nsv522873 CNV Gain 19592680
nsv9793 CNV Gain+Loss 18304495
nsv833946 CNV Gain 17160897
esv2662588 CNV Deletion 23128226
esv2673324 CNV Deletion 23128226
nsv178771 CNV Loss 16902084
esv2540968 CNV Insertion 19546169
nsv513540 CNV Insertion 21212237
esv1529124 CNV Insertion 17803354
nsv179076 CNV Loss 16902084
esv990034 CNV Loss 20482838
esv2657114 CNV Deletion 23128226
nsv912824 CNV Gain 21882294
nsv524920 CNV Gain 19592680
esv2651577 CNV Insertion 19546169

Relevant External Links for SYNDIG1 Gene

HapMap Linkage Disequilibrium report

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for SYNDIG1 Gene

Disorders for SYNDIG1 Gene

No disorders were found for SYNDIG1 Gene.

No data available for UniProtKB/Swiss-Prot for SYNDIG1 Gene

Publications for SYNDIG1 Gene

  1. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T. … Sugano S. (Nat. Genet. 2004) 3 4
  2. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard D.S. … Malek J. (Genome Res. 2004) 3 4
  3. The DNA sequence and comparative analysis of human chromosome 20. (PMID: 11780052) Deloukas P. … Rogers J. (Nature 2001) 3 4
  4. SynDIG1: an activity-regulated, AMPA- receptor-interacting transmembrane protein that regulates excitatory synapse development. (PMID: 20152115) Kalashnikova E. … DA-az E. (Neuron 2010) 2 3
  5. The dispanins: a novel gene family of ancient origin that contains 14 human members. (PMID: 22363774) Sallman Almen M. … Schioth H.B. (PLoS ONE 2012) 3 4

Products for SYNDIG1 Gene

Sources for SYNDIG1 Gene

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