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Category   Symbol Source: HGNC EntrezGene Ensembl GeneCards RNA genes CroW21
GIFtS

SYNDIG1 Gene

protein-coding   GIFtS: 41
GCID: GC20P024451

Synapse Differentiation Inducing 1

(Previous names: chromosome 20 open reading frame 39, transmembrane protein...)
(Previous symbols: C20orf39, TMEM90B)
  Search for SYNDIG1
at  

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
About This Section

Aliases
Synapse Differentiation Inducing 11 2     Dispanin Subfamily C Member 22 3
Transmembrane Protein 90B1 2 3     DSPC22 3
C20orf391 2 3     Chromosome 20 Open Reading Frame 391
TMEM90B1 2 3     IFITMD52
Interferon Induced Transmembrane Protein Domain Containing 51 2     Synapse Differentiation-Inducing Gene Protein 12
Synapse Differentiation Induced Gene 11 2     SynDIG13

External Ids:    HGNC: 158851   Entrez Gene: 799532   Ensembl: ENSG000001014637   OMIM: 6143115   UniProtKB: Q9H7V23   

Export aliases for SYNDIG1 gene to outside databases


(According to Entrez Gene, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
About This Section

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 glutamate receptor binding and protein homodimerization activity. An important paralog of this gene is SYNDIG1L.

UniProtKB/Swiss-Prot: SYNG1_HUMAN, Q9H7V2
Function: May regulate AMPA receptor content at nascent synapses, and have a role in postsynaptic development and
maturation (By similarity)




(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 73), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section
RefSeq DNA sequence:
NC_000020.10  NT_011387.8  NC_018931.2  
Regulatory elements:
   Search SABiosciences Regulatory transcription factor binding sites for SYNDIG1
         Other transcription factors

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Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat SYNDIG1


Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: 20p11.21   Ensembl cytogenetic band:  20p11.21   HGNC cytogenetic band: 20p11.21

SYNDIG1 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
SYNDIG1 gene location

GeneLoc information about chromosome 20         GeneLoc Exon Structure

GeneLoc location for GC20P024451:  view genomic region     (about GC identifiers)

Start:
24,449,835 bp from pter      End:
24,647,252 bp from pter
Size:
197,418 bases      Orientation:
plus strand

(According to UniProtKB, HORDE, neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MAXQB RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, and/or Cloud-Clone Corp.,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Cloud-Clone Corp., Ontologies according to Gene Ontology Consortium 01 Oct 2013 and Entrez Gene, Antibodies by EMD Millipore, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, and/or Cloud-Clone Corp.)
About This Section

UniProtKB/Swiss-Prot: SYNG1_HUMAN, Q9H7V2 (See protein sequence)
Recommended Name: Synapse differentiation-inducing gene protein 1  
Size: 258 amino acids; 28551 Da
Subunit: Homodimer. Interacts with GRIA1 and GRIA2 (By similarity)
Subcellular location: Cell membrane; Single-pass type II membrane protein. Early endosome membrane; Single-pass
type II membrane protein (By similarity). Cell junction, synapse, postsynaptic cell membrane, postsynaptic
density (By similarity). Cell junction, synapse (By similarity). Cell projection, dendrite (By similarity). Cell
projection, dendritic spine (By similarity). Note=Shuttles between the cell surface and early endosome membrane
(By similarity)
Secondary accessions: Q6IA30 Q9H514

Explore the universe of human proteins at neXtProt for SYNDIG1: NX_Q9H7V2

Explore proteomics data for SYNDIG1 at MOPED 

Post-translational modifications:

  • View modification sites using PhosphoSitePlus
  • View neXtProt modification sites for NX_Q9H7V2

  • SYNDIG1 Protein expression data from MOPED1, PaxDb2 and MAXQB3 :    About this image 

    SYNDIG1 Protein Expression
    REFSEQ proteins: NP_079169.1  
    ENSEMBL proteins: 
     ENSP00000366058  

    Human Recombinant Protein Products for SYNDIG1: 
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    Cloud-Clone Corp. Proteins for SYNDIG1 

    Gene Ontology (GO): 5/10 cellular component terms (GO ID links to tree view) (see all 10):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005887integral to plasma membrane ISS--
    GO:0014069postsynaptic density ISS--
    GO:0016021integral to membrane ----
    GO:0030054cell junction IEA--
    GO:0031901early endosome membrane ISS--

    SYNDIG1 for ontologies           About GeneDecksing



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    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
    About This Section
    1 InterPro protein domain:
     IPR007593 Interferon-induced_TM_protein

    Graphical View of Domain Structure for InterPro Entry Q9H7V2

    ProtoNet protein and cluster: Q9H7V2

    UniProtKB/Swiss-Prot: SYNG1_HUMAN, Q9H7V2
    Similarity: Belongs to the CD225/Dispanin family


    SYNDIG1 for domains           About GeneDecksing


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, inGenious Targeting Laboratory, genOway,
    bound targets from SABiosciences, miRNA Gene Targets from miRTarBase, shRNA from OriGene, RNAi from EMD Millipore, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, Gene Editing from DNA2.0, Sirion Biotech, Clones from EMD Millipore, OriGene, SwitchGear Genomics, GenScript, Sino Biological, DNA2.0, Vector BioLabs, and Sirion Biotech, Cell Lines from GenScript, LifeMap BioReagents, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Oct 2013 via Entrez Gene.)
    About This Section

    Molecular Function:

         UniProtKB/Swiss-Prot Summary: SYNG1_HUMAN, Q9H7V2
    Function: May regulate AMPA receptor content at nascent synapses, and have a role in postsynaptic development and
    maturation (By similarity)

         Gene Ontology (GO): 2 molecular function terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0035254glutamate receptor binding ISS--
    GO:0042803protein homodimerization activity ISS--
         
    SYNDIG1 for ontologies           About GeneDecksing


    Animal Models:
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    (Pathways according to EMD Millipore, R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Sino Biological, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to SABiosciences, and/or STRING, Interactions according to 1UniProtKB, 2MINT, 3I2D, and/or 4STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Oct 2013 via Entrez Gene).
    About This Section



    Interactions:

        Search SABiosciences Gene Network CentralTM Interacting Genes and Proteins Networks for SYNDIG1

    1 Interacting protein for SYNDIG1 (Q9H7V22, 3) via UniProtKB, MINT, STRING, and/or I2D
    InteractantInteraction Details
    GeneCardExternal ID(s)
    PFDN1O609252, 3MINT-63195 I2D: score=4 
    About this table

    Gene Ontology (GO): 4 biological process terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0006886intracellular protein transport ISS--
    GO:0009607response to biotic stimulus IEA--
    GO:0051965positive regulation of synapse assembly IDA--
    GO:0097091synaptic vesicle clustering ISS--

    SYNDIG1 for ontologies           About GeneDecksing



    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB, with drugs/clinical trials/news search links to CenterWatch)
    About This Section
    Browse Small Molecules at EMD Millipore
    Browse drugs & compounds from Enzo Life Sciences

    Browse Tocris compounds for SYNDIG1 (SYNG1)

    Search CenterWatch for drugs/clinical trials and news about SYNDIG1 / SYNG1

    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 236 Homo sapiens; Apr 25 2013) or GenBank,
    RefSeq according to Entrez Gene,
    DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
    Conferences by KenesGroup, exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
    RNAi Products from EMD Millipore,
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    Tagged/untagged cDNA clones from OriGene, SwitchGear Genomics, GenScript, DNA2.0, Vector BioLabs, Sirion Biotech, Primers from OriGene, SABiosciences, and/or QIAGEN )
    About This Section

    REFSEQ mRNAs for SYNDIG1 gene: 
    NM_024893.2  

    Unigene Cluster for SYNDIG1:

    Synapse differentiation inducing 1
    Hs.124638  [show with all ESTs]
    Unigene Representative Sequence: AK024282
    2 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000376862(uc002wtw.1) ENST00000482637
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    Additional mRNA sequence: 

    AK024282.1 BC030637.1 CR457325.1 

    5 DOTS entries:

    DT.311488  DT.95371357  DT.91640628  DT.97765037  DT.120818819 

    24/81 AceView cDNA sequences (see all 81):

    AK024282 AI002454 F06074 BF344176 AI568140 NM_024893 BU154434 Z38996 
    BF449019 AI366047 BF116046 AI333224 T16541 F05199 AI868234 BM690090 
    BM666809 F07165 Z40543 BM695022 F01451 BX951905 BM925405 AI363429 

    GeneLoc Exon Structure


    (RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, plus additional links to Genevestigator, and/or SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from SABiosciences, Primers from OriGene, SABiosciences, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
    About This Section

    SYNDIG1 expression in normal human tissues (normalized intensities)      SYNDIG1 embryonic expression: see
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: CTGCTTAAGT
    SYNDIG1 Expression
    About this image


    SYNDIG1 expression in embryonic tissues and stem cells    About this table
    Data from LifeMap, the Embryonic Development and Stem Cells Database 
     5/9 selected tissues (see all 9) fully expand
     
     Uncategorized (Uncategorized)    fully expand to see all 5 entries
             PureStem Progenitor EN7
     
     Brain (Nervous System)    fully expand to see all 3 entries
             Human Cerebellar Astrocytes   
             cerebellum   
     
     Bone (Muscoskeletal System)    fully expand to see all 3 entries
             HyStem+TGFbeta3+GDF5-induced SK11 cells
     
     Cartilage (Muscoskeletal System)    fully expand to see all 3 entries
             HyStem+TGFbeta3+GDF5-induced SK11 cells
     
     Neural Crest (Gastrulation Derivatives)
             PureStem SM30, NCr-fac & Meso-latp Progenitor

    See SYNDIG1 Protein Expression from SPIRE MOPED and PaxDB
    Genevestigator expression for SYNDIG1

    SOURCE GeneReport for Unigene cluster: Hs.124638
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    In Situ
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    (Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD , 5MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or 6Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
    About This Section

    This gene was present in the common ancestor of chordates.

    Orthologs for SYNDIG1 gene from 4/10 species (see all 10)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Syndig15
    Tmem90b1
    transmembrane protein 90B1, 5 87.73(n)1
    93.02(a)1
      2 (73.80 cM)5
    4334851  NM_001085521.21  NP_001078990.11 
     1498292115 
    chicken
    (Gallus gallus)
    Aves SYNDIG11 synapse differentiation inducing 1 80.99(n)
    86.33(a)
      416717  XM_415014.3  XP_415014.2 
    lizard
    (Anolis carolinensis)
    Reptilia SYNDIG16
    Uncharacterized protein
    78(a)
    1 ↔ 1
    4(79834745-79875090)
    zebrafish
    (Danio rerio)
    Actinopterygii LOC7925531 transmembrane protein 90B-like 73.68(n)
    73.82(a)
      792553  XM_001332064.4  XP_001332100.2 


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

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
    About This Section
    Paralogs for SYNDIG1 gene
    SYNDIG1L2  TMEM912  
    1 SIMAP similar gene for SYNDIG1 using alignment to 1 protein entry:     SYNG1_HUMAN:
    SYNDIG1L

    SYNDIG1 for paralogs           About GeneDecksing



    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, 4UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD) and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers from QIAGEN, Cancer Mutation PCR Arrays and Assays and Copy Number PCR Arrays from SABiosciences)
    About This Section

    10/4240 SNPs in SYNDIG1 are shown (see all 4240)    About this table     
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 20 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs766005811,2
    C,F--24447847(+) GGCCAC/GAGGAC 1 -- us2k12Minor allele frequency- G:0.09NA EA 240
    rs1825922951,2
    --24447981(+) TTGCTC/TGGTGC 1 -- us2k10--------
    rs1869218411,2
    --24448013(+) CACAGA/GAGGTG 1 -- us2k10--------
    rs1922720461,2
    --24448029(+) CAGACC/TTCTCT 1 -- us2k10--------
    rs1409918001,2
    --24448090(+) GGTTAA/CCCCAG 1 -- us2k10--------
    rs1446817601,2
    --24448168(+) TCTTGA/TAAGTC 1 -- us2k10--------
    rs1479351011,2
    --24448250(+) AAACTA/GCCCAT 1 -- us2k10--------
    rs1154188461,2
    F--24448314(+) CTGCCA/GGGAGT 1 -- us2k11Minor allele frequency- G:0.02WA 118
    rs19977891,2
    C,F,H--24448347(+) TACACG/ATCCTG 1 -- us2k16Minor allele frequency- A:0.01NS NA WA 626
    rs356974291,2
    C--24448408(+) AAGAT-/TG    
       
    /TGTG
    GTGTG
    1 -- us2k10--------

    HapMap Linkage Disequilibrium report for SYNDIG1 (24449835 - 24647252 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 10/15 variations for SYNDIG1 (see all 15):    About this table     
    Variant IDTypeSubtypePubMed ID
    esv2673324CNV Deletion23128226
    esv2657114CNV Deletion23128226
    esv2662588CNV Deletion23128226
    esv1529124CNV Insertion17803354
    esv2540968CNV Insertion19546169
    esv2651577CNV Insertion19546169
    nsv513540CNV Insertion21212237
    nsv179076CNV Loss16902084
    esv990034CNV Loss20482838
    nsv178771CNV Loss16902084

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    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Conferences by KenesGroup, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
    About This Section

    SYNDIG1 for disorders           About MalaCards
    OMIM gene information: 614311    OMIM disorders: --


    SYNDIG1 for disorders           About GeneDecksing


    Export disorders for SYNDIG1 gene to outside databases

    (in PubMed. Associations of this gene to articles via 1Entrez Gene, 2UniProtKB/Swiss-Prot, 3HGNC, 4GAD, 5PharmGKB, 6HMDB, 7DrugBank, 8UniProtKB/TrEMBL, 9 Novoseek, and/or 10fRNAdb)
    About This Section

    PubMed articles for SYNDIG1 gene integrated from 9 sources:
    (articles sorted by number of sources associating them with SYNDIG1)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. SynDIG1: an activity-regulated, AMPA- receptor-intera cting transmembrane protein that regulates excitatory synapse development. (PubMed id 20152115)1, 3 Kalashnikova E....DA-az E. (2010)
    2. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)1, 2 Gerhard D.S....Malek J. (2004)
    3. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1, 2 Ota T.... Sugano S. (2004)
    4. The DNA sequence and comparative analysis of human chromosome 20. (PubMed id 11780052)1, 2 Deloukas P....Rogers J. (2001)
    5. The dispanins: a novel gene family of ancient origin that contains 14 human members. (PubMed id 22363774)2 Sallman Almen M.... Schioth H.B. (2012)
    6. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. (PubMed id 20379614)1 Rose J.E....Uhl G.R. (2010)
    7. hORFeome v3.1: a resource of human open reading frames representing over 10,000 human genes. (PubMed id 17207965)1 Lamesch P.... Vidal M. (2007)
    8. Diversification of transcriptional modulation: large-scale identification and characterization of putative alternative promoters of human genes. (PubMed id 16344560)1 Kimura K.... Sugano S. (2006)
    9. A human protein-protein interaction network: a resource for annotating the proteome. (PubMed id 16169070)1 Stelzl U.... Wanker E.E. (2005)
    10. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. (PubMed id 12477932)1 Strausberg R.L....Marra M.A. (2002)

    (in PubMed, OMIM, and NCBI Bookshelf)
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    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
    About This Section
    Entrez Gene: 79953 HGNC: 15885 AceView: C20orf39 Ensembl:ENSG00000101463 euGenes: HUgn79953
    ECgene: SYNDIG1 H-InvDB: SYNDIG1

    (According to HUGE)
    About This Section
      --

    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
    Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot)
    About This Section
    NameDescription
    PharmGKB entry for SYNDIG1 Pharmacogenomics, SNPs, Pathways

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
    About This Section
    Patent Information for SYNDIG1 gene:
    Search GeneIP for patents involving SYNDIG1

    GeneCards and IP:
    Japan Patent Office Licenses GeneCards     European Patent Office Licenses GeneCards     Improving the IP Search



    (Antibodies, recombinant proteins, and assays from EMD Millipore, R&D Systems, OriGene, QIAGEN, GenScript, Cell Signaling Technology, SABiosciences, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Cloud-Clone Corp., Thermo Fisher Scientific, LSBio, Gene Editing from DNA2.0 and Sirion Biotech, Clones from EMD Millipore, OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Sirion Biotech, Cell lines from GenScript, and LifeMap BioReagents, PCR Arrays from SABiosciences, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, and/or Enzo Life Sciences, In Situ Hybridization Assays from
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    GeneCards Homepage - Last full update: 23 Oct 2013 - Incrementals: 4 Nov 2013 , 7 Nov 2013 , 23 Jan 2014

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