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SYNDIG1L Gene

protein-coding   GIFtS: 35
GCID: GC14M074873

Synapse Differentiation Inducing 1-Like

(Previous name: transmembrane protein 90A)
(Previous symbol: TMEM90A)
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(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
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Aliases
Synapse Differentiation Inducing 1-Like1 2     DSPC12 3
TMEM90A1 2 3 5     CAPUCIN2 5
Transmembrane Protein 90A1 2 3     IFITMD42
Caudate-And Putamen-Enriched Sequence1 2     Caudate- And Putamen-Enriched Sequence2
Interferon Induced Transmembrane Protein Domain Containing 41 2     Synapse Differentiation-Inducing Gene Protein 1-Like2
Dispanin Subfamily C Member 12 3     Capucin3

External Ids:    HGNC: 323881   Entrez Gene: 6466582   Ensembl: ENSG000001833797   OMIM: 6099995   UniProtKB: A6NDD53   

Export aliases for SYNDIG1L gene to outside databases


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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GeneCards Summary for SYNDIG1L Gene:
SYNDIG1L (synapse differentiation inducing 1-like) is a protein-coding gene. An important paralog of this gene is TMEM91.


(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 75), Regulatory elements and Epigenetics data according to QIAGEN, and/or SwitchGear Genomics)
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RefSeq DNA sequence at NCBI GenBank:
NC_000014.8  NC_018925.2  NT_026437.13  
Regulatory elements:
   Search for regulatory transcription factor binding sites for SYNDIG1L
         Other transcription factors

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Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat SYNDIG1L


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

Entrez Gene cytogenetic band: 14q24.3   Ensembl cytogenetic band:  14q24.3   HGNC cytogenetic band: 14q24.3

SYNDIG1L Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
SYNDIG1L gene location

GeneLoc information about chromosome 14         GeneLoc Exon Structure

GeneLoc location for GC14M074873:  view genomic region     (about GC identifiers)

Start:
74,872,596 bp from pter      End:
74,892,805 bp from pter
Size:
20,210 bases      Orientation:
minus strand

(According to 1UniProtKB, HORDE, 2neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, 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, Cloud-Clone Corp., and/or eBioscience,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, Cloud-Clone Corp., and/or eBioscience, Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, Cloud-Clone Corp, and/or others.)
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UniProtKB/Swiss-Prot: SYN1L_HUMAN, A6NDD5 (See protein sequence)
Recommended Name: Synapse differentiation-inducing gene protein 1-like  
Size: 238 amino acids; 25796 Da

Explore the universe of human proteins at neXtProt for SYNDIG1L: NX_A6NDD5

Explore proteomics data for SYNDIG1L at MOPED


See SYNDIG1L Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

REFSEQ proteins: NP_001099049.1  
ENSEMBL proteins: 
 ENSP00000450439   ENSP00000451519   ENSP00000331474  

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(According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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1 InterPro protein domain:
 IPR007593 CD225/Dispanin_fam

Graphical View of Domain Structure for InterPro Entry A6NDD5

ProtoNet protein and cluster: A6NDD5

UniProtKB/Swiss-Prot: SYN1L_HUMAN, A6NDD5
Similarity: Belongs to the CD225/Dispanin family


Find genes that share domains with SYNDIG1L           About GenesLikeMe


(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,
transcription factor targeting from QIAGEN and/or HOMER, miRNA Gene Targets from miRTarBase, shRNA from OriGene, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, SwitchGear Genomics, Gene Editing from DNA2.0, Clones from OriGene, GenScript, Sino Biological, DNA2.0, Vector BioLabs and/or Addgene, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Flow cytometry from eBioscience, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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Phenotypes:
     2 MGI mutant phenotypes (inferred from 1 allele(MGI details for Syndig1l):
 nervous system  reproductive system 

Find genes that share phenotypes with SYNDIG1L           About GenesLikeMe

Animal Models:
     MGI mouse knock-out Syndig1ltm1Embr for SYNDIG1L

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hsa-mir-132-3p (MIRT021797)

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hsa-miR-548a-3p hsa-miR-654-5p hsa-miR-491-5p hsa-miR-205* hsa-miR-548e hsa-miR-1205 hsa-miR-541
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(According to UniProtKB, COMPARTMENTS Subcellular localization database, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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Subcellular locations from UniProtKB/Swiss-Prot
SYN1L_HUMAN, A6NDD5: Membrane; Multi-pass membrane protein (Potential). Golgi apparatus, cis-Golgi network (By
similarity)

Gene Ontology (GO): 2 cellular component terms:    About this table

GO IDQualified GO termEvidencePubMed IDs
GO:0005794Golgi apparatus IEA--
GO:0016021integral component of membrane IEA--

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(SuperPaths according to PathCards, Pathways according to 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 QIAGEN, 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 Apr 2014 via Entrez Gene).
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    Custom Pathway & Disease-focused RT2 Profiler PCR Arrays for SYNDIG1L
Interactions:

    Search GeneGlobe Interaction Network for SYNDIG1L

Gene Ontology (GO): 1 biological process term:    About this table

GO IDQualified GO termEvidencePubMed IDs
GO:0009607response to biotic stimulus IEA--

Find genes that share ontologies with SYNDIG1L           About GenesLikeMe



(Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience, ApexBio, HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB)
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Browse Small Molecules at EMD Millipore
   Browse drugs & compounds from Enzo Life Sciences
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Browse Tocris compounds for SYNDIG1L (SYN1L)



(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,
exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN, SwitchGear Genomics,
Tagged/untagged cDNA clones from OriGene, GenScript, DNA2.0, Vector BioLabs, and/or Addgene, Primers from OriGene, and/or QIAGEN, Flow cytometry from eBioscience )
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REFSEQ mRNAs for SYNDIG1L gene: 
NM_001105579.1  

Unigene Cluster for SYNDIG1L:

Synapse differentiation inducing 1-like
Hs.12400  [show with all ESTs]
Unigene Representative Sequence: NM_001105579
3 Ensembl transcripts including schematic representations, and UCSC links where relevant:
ENST00000554823 ENST00000554953 ENST00000331628(uc001xpx.2)
miRNA
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hsa-miR-548a-3p hsa-miR-654-5p hsa-miR-491-5p hsa-miR-205* hsa-miR-548e hsa-miR-1205 hsa-miR-541
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  QuantiFast Probe-based Assays in human, mouse, rat SYNDIG1L

Additional mRNA sequence: 

AK094873.1 BC030107.2 BC045804.1 

3 DOTS entries:

DT.427170  DT.106401  DT.95184328 

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™, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MaxQB, plus additional links to SOURCE, and/or BioGPS, and/or UniProtKB,
PCR Arrays from QIAGEN, Primers from OriGene, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
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SYNDIG1L expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS <intensity>2/3
CGAP TAG: CCCCATCCAG
SYNDIG1L Expression
About this image


SYNDIG1L expression in embryonic tissues and stem cells    About this table
Data from LifeMap, the Embryonic Development and Stem Cells Database
 
 Brain (Nervous System)    fully expand to see all 22 entries
         Thalamus
         Substantia Nigra   
SYNDIG1L Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

SYNDIG1L Protein Expression

SOURCE GeneReport for Unigene cluster: Hs.12400
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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)
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This gene was present in the common ancestor of chordates.

Orthologs for SYNDIG1L gene from Selected species (see all 9)    About this table
Organism Taxonomic
classification
Gene Description Human
Similarity
Orthology
Type
Details
mouse
(Mus musculus)
Mammalia Syndig1l1 , 5 transmembrane protein 90a5
synapse differentiation inducing 1 like1
86.22(n)1
87.76(a)1
  12 (39.33 cM)5
6271911  NM_001033334.21  NP_001028506.11 
 846772785 
chicken
(Gallus gallus)
Aves SYNDIG1L1 synapse differentiation inducing 1-like 68.55(n)
60.87(a)
  423351  XM_421266.4  XP_421266.2 
lizard
(Anolis carolinensis)
Reptilia SYNDIG1L6
synapse differentiation inducing 1-like
59(a)
1 ↔ 1
1(23388996-23409335)
zebrafish
(Danio rerio)
Actinopterygii syndig1l1 synapse differentiation inducing 1-like 62.03(n)
56.52(a)
  555204  NM_001044781.1  NP_001038246.1 


ENSEMBL Gene Tree for SYNDIG1L (if available)
TreeFam Gene Tree for SYNDIG1L (if available)

(Paralogs according to 1HomoloGene,
2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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Paralogs for SYNDIG1L gene
TMEM912  SYNDIG12  
2 SIMAP similar genes for SYNDIG1L using alignment to 2 protein entries:     SYN1L_HUMAN (see all proteins):
SYNDIG1    TMEM91

Find genes that share paralogs with SYNDIG1L           About GenesLikeMe



(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), the Human Cytochrome P450 Allele Nomenclature Database, and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers, Cancer Mutation PCR Arrays and Assays, and Copy Number PCR Arrays from QIAGEN)
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Selected SNPs for SYNDIG1L (see all 509)    About this table                                 

Genomic DataTranscription Related DataAllele Frequencies
SNP IDValidClinical
significance
Chr 14 posSequence#AA
Chg
TypeMore#Allele
freq
PopTotal
sample
More
----------
rs596804801,2
C--55056724(+) ACACA-/CA/CACACACACAC/CACACA
CACACA
/CACACACACACACACA
ATTTC
2 -- int1 cds10--------
rs673907101,2
C--55056724(-) GAAAT-/TGTGTGT 1 -- int11Minor allele frequency- TG:0.00NA 2
rs49032231,2
C,F,A,H--74872145(+) CACATT/GGTCCA 1 -- int122Minor allele frequency- G:0.41NA NS EA WA CSA 1350
rs1175763061,2
F--74872155(+) AGGAGC/TGGCTC 1 -- int11Minor allele frequency- T:0.01EA 120
rs111590781,2
C,F,A,H--74872187(+) AGGAGC/TAGGCA 1 -- int114Minor allele frequency- T:0.35NS EA NA WA 766
rs1834824321,2
--74872193(+) AGGCAA/GCAGGG 1 -- int10--------
rs1489246401,2
C--74872289(+) CATCCA/CTTCCT 1 -- int10--------
rs756720811,2
F--74872343(+) AGGCAC/TGGATC 1 -- int11Minor allele frequency- T:0.05NA 120
rs1852885011,2
--74872471(+) CATACA/GTGGGC 1 -- int10--------
rs1470269671,2
--74872562(+) AAAGGC/TGGGGC 1 -- int10--------

HapMap Linkage Disequilibrium report for SYNDIG1L (74872596 - 74892805 bp)

Structural Variations
     Database of Genomic Variants (DGV) 2 variations for SYNDIG1L:    About this table    
Variant IDTypeSubtypePubMed ID
nsv832829CNV Loss17160897
esv33960CNV Gain17666407

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(in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
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OMIM gene information: 609999    OMIM disorders: --


Find genes that share disorders with SYNDIG1L           About GenesLikeMe


Export disorders for SYNDIG1L 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)
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PubMed articles for SYNDIG1L gene integrated from 10 sources:
(articles sorted by number of sources associating them with SYNDIG1L)
    Utopia: connect your pdf to the dynamic
world of online information

  1. Capucin: a novel striatal marker down-regulated in rodent models of Huntington disease. (PubMed id 16359841)1, 2, 3 de Chaldee M.... Elalouf J.-M. (Genomics 2006)
  2. The dispanins: a novel gene family of ancient origin that contains 14 human members. (PubMed id 22363774)1, 2 Sallman Almen M.... Schioth H.B. (PLoS ONE 2012)
  3. Diversification of transcriptional modulation: large-scale identification and characterization of putative alternative promoters of human genes. (PubMed id 16344560)1 Kimura K.... Sugano S. (Genome Res. 2006)
  4. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1 Ota T.... Sugano S. (Nat. Genet. 2004)
  5. The DNA sequence and analysis of human chromosome 14. (PubMed id 12508121)2 Heilig R.... Weissenbach J. (Nature 2003)
  6. 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. (Proc. Natl. Acad. Sci. U.S.A. 2002)

(in PubMed, OMIM, and NCBI Bookshelf)
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 ANDOR
Aliases
Free Text  

  Query String
PubMed
OMIM
NCBI Bookshelf
  (Note: In FireFox, select the above section and copy using Ctrl-C)

(According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
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Entrez Gene: 646658 HGNC: 32388 Ensembl:ENSG00000183379 euGenes: HUgn646658 ECgene: SYNDIG1L
H-InvDB: SYNDIG1L

(According to HUGE)
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  --

(According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, and/or others, e.g. Wikipedia and GeneReviews, via UniProtKB/Swiss-Prot)
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NameDescription
PharmGKB entry for SYNDIG1L Pharmacogenomics, SNPs, Pathways

(Patent information from GeneIP,
Licensable technologies from WIS Yeda, Salk, Tufts,
IP news from LifeMap Sciences, Inc.)
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Patent Information for SYNDIG1L gene:
Search GeneIP for patents involving SYNDIG1L

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, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Cloud-Clone Corp., Thermo Fisher Scientific, LSBio, eBioscience, and/or others, Gene Editing from DNA2.0. Clones from OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Addgene, Cell lines from GenScript, and ESI BIO, Flow cytometery from eBioscience, PCR Arrays from QIAGEN, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, Enzo Life Sciences, and/or ApexBio, In Situ Hybridization Assays from
Advanced Cell Diagnostics, Animal models from inGenious Targeting Laboratory, genOway)
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GeneCards Homepage - Last full update: 7 May 2014 - Incrementals: 9 May 2014 , 2 Jun 2014 , 26 Jun 2014 , 30 Jun 2014 , 21 Aug 2014 , 8 Sep 2014

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