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

SYNDIG1L Gene

protein-coding   GIFtS: 34
GCID: GC14M074873

Synapse Differentiation Inducing 1-Like

(Previous name: transmembrane protein 90A)
(Previous symbol: TMEM90A)
  See related disease
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 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, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
About This Section

GeneCards Summary for SYNDIG1L Gene: 
SYNDIG1L (synapse differentiation inducing 1-like) is a protein-coding gene. Diseases associated with SYNDIG1L include huntington's disease. 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 73), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section
RefSeq DNA sequence:
NC_000014.8  NC_018925.2  NT_026437.12  
Regulatory elements:
   Search SABiosciences Regulatory transcription factor binding sites for SYNDIG1L
         Other transcription factors

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Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays 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 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: SYN1L_HUMAN, A6NDD5 (See protein sequence)
Recommended Name: Synapse differentiation-inducing gene protein 1-like  
Size: 238 amino acids; 25796 Da
Subcellular location: Membrane; Multi-pass membrane protein (Potential). Golgi apparatus, cis-Golgi network (By
similarity)

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

Explore proteomics data for SYNDIG1L at MOPED 

SYNDIG1L Protein expression data from MOPED1, PaxDb2 and MAXQB3 :    About this image 

SYNDIG1L Protein Expression

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

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

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

SYNDIG1L 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 A6NDD5

ProtoNet protein and cluster: A6NDD5

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


SYNDIG1L 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

Phenotypes:
     2 MGI mutant phenotypes (inferred from 1 allele(MGI details for Syndig1l):
 nervous system  reproductive system 

SYNDIG1L for phenotypes           About GeneDecksing

Animal Models:
     MGI mouse knock-out Syndig1ltm1Embr for SYNDIG1L

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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 SYNDIG1L

Gene Ontology (GO): 1 biological process term (GO ID links to tree view):    About this table

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

SYNDIG1L 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
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Search CenterWatch for drugs/clinical trials and news about 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,
Conferences by KenesGroup, exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
RNAi Products from EMD Millipore,
siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN,
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 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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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™, 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

SYNDIG1L expression in normal human tissues (normalized intensities)      SYNDIG1L embryonic expression: see
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 
 5/2 selected tissues (see all 2) fully expand
 
 Brain (Nervous System)    fully expand to see all 22 entries
         Thalamus
         Substantia Nigra   
 
 Spinal Cord (Nervous System)    fully expand to see all 3 entries
         Dorsal Horn   

See SYNDIG1L Protein Expression from SPIRE MOPED and PaxDB
Genevestigator expression for SYNDIG1L

SOURCE GeneReport for Unigene cluster: Hs.12400
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In Situ
Assay Products:
 

 
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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 SYNDIG1L gene from 4/9 species (see all 9)    About this table
Organism Taxonomic
classification
Gene Description Human
Similarity
Orthology
Type
Details
mouse
(Mus musculus)
Mammalia Syndig1l5
Tmem90a1
transmembrane protein 90a1, 5 86.78(n)1
89.03(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 67.97(n)
60.87(a)
  423351  XM_421266.3  XP_421266.1 
lizard
(Anolis carolinensis)
Reptilia SYNDIG1L6
Uncharacterized protein
58(a)
1 ↔ 1
1(23388996-23409335)
zebrafish
(Danio rerio)
Actinopterygii syndig1l1 synapse differentiation inducing 1-like 62.75(n)
57.39(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)
About This Section
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

SYNDIG1L 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

10/509 SNPs in SYNDIG1L are shown (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, Conferences by KenesGroup, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
About This Section
OMIM gene information: 609999    OMIM disorders: --

2 diseases for SYNDIG1L:    About MalaCards
huntington's disease    


SYNDIG1L for disorders           About GeneDecksing


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)
About This Section

PubMed articles for SYNDIG1L gene integrated from 9 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. (2006)
  2. 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)
  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. (2006)
  4. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1 Ota T.... Sugano S. (2004)
  5. The DNA sequence and analysis of human chromosome 14. (PubMed id 12508121)2 Heilig R.... Weissenbach J. (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. (2002)

(in PubMed, OMIM, and NCBI Bookshelf)
About This Section
 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)
About This Section
Entrez Gene: 646658 HGNC: 32388 Ensembl:ENSG00000183379 euGenes: HUgn646658 ECgene: SYNDIG1L
H-InvDB: SYNDIG1L

(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 SYNDIG1L 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 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, 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
Advanced Cell Diagnostics, Animal models from inGenious Targeting Laboratory, genOway)
About This Section

 
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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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transforming growth factor, beta 1
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