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SYS1-DBNDD2 Gene

protein-coding   GIFtS: 22
GCID: GC20P043991

SYS1-DBNDD2 Readthrough (NMD Candidate)

(Previous name: SYS1-DBNDD2 readthrough (non-protein coding))
  Search for SYS1-DBNDD2
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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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This gene clusters with an RNA gene
Subcategory (RNA class): antisense

Quality score for the ORGUL clustered with this gene is 3

Aliases
SYS1-DBNDD2 Readthrough (NMD Candidate)1 2
SYS1-DBNDD2 Readthrough (Non-Protein Coding)1
C20orf169-DBNDD22

External Ids:    HGNC: 335351   Entrez Gene: 7675572   Ensembl: ENSG000002548067   UniProtKB: F2Z2A34   UniProtKB: H3BUS14   
ORGUL members:         

Export aliases for SYS1-DBNDD2 gene to outside databases

Previous GC identifers: GC20U900295 GC20P043427


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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Entrez Gene summary for SYS1-DBNDD2 Gene:
This locus represents naturally occurring read-through transcription from the neighboring SYS1 Golgi-localized
integral membrane protein homolog and dysbindin domain containing 2 (DBNDD2) genes. The read-through transcript
includes the majority of exons from each individual gene, but it would be subject to nonsense-mediated mRNA decay
(NMD) and is therefore predicted to be non-coding. (provided by RefSeq, Oct 2010)

GeneCards Summary for SYS1-DBNDD2 Gene:
SYS1-DBNDD2 (SYS1-DBNDD2 readthrough (NMD candidate)) is a protein-coding gene. An important paralog of this gene is SYS1.




(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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Regulatory elements:
   Regulatory transcription factor binding sites in the SYS1-DBNDD2 gene promoter:
         AP-1   ATF-2   MyoD   c-Jun   NF-kappaB1   NF-kappaB   
         Other transcription factors

Browse SwitchGear Promoter luciferase reporter plasmids
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Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat SYS1-DBNDD2


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

Entrez Gene cytogenetic band: 20q13.12   Ensembl cytogenetic band:  20q13.12   HGNC cytogenetic band: 20q13.12

SYS1-DBNDD2 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
SYS1-DBNDD2 gene location

GeneLoc information about chromosome 20         GeneLoc Exon Structure

GeneLoc location for GC20P043991:  view genomic region     (about GC identifiers)

Start:
43,991,809 bp from pter      End:
44,039,250 bp from pter
Size:
47,442 bases      Orientation:
plus 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, 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., 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/TrEMBL: F2Z2A3 (See protein sequence)
Recommended Name: Protein SYS1-DBNDD2  
Size: 78 amino acids; 8717 Da
Caution: The sequence shown here is derived from an Ensembl automatic analysis pipeline and should be considered
as preliminary data

UniProtKB/TrEMBL: H3BUS1 (See protein sequence)

Recommended Name: Protein SYS1-DBNDD2  
Size: 97 amino acids; 11030 Da
Caution: The sequence shown here is derived from an Ensembl automatic analysis pipeline and should be considered
as preliminary data


ENSEMBL proteins: 
 ENSP00000456116   ENSP00000457768   ENSP00000457650  

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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:
 IPR019185 Integral_membrane_SYS1-rel

Graphical View of Domain Structure for InterPro Entry F2Z2A3
Graphical View of Domain Structure for InterPro Entry H3BUS1

ProtoNet protein and cluster: F2Z2A3


SYS1-DBNDD2 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,
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, and Vector BioLabs, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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Animal Models:
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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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  --

(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 SYS1-DBNDD2
Interactions:

    Search GeneGlobe Interaction Network for SYS1-DBNDD2

(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 SYS1-DBNDD2



(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, Primers from OriGene, and/or QIAGEN )
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4 Ensembl transcripts including schematic representations, and UCSC links where relevant:
ENST00000419593(uc002xnx.3) ENST00000475242 ENST00000458187 ENST00000452133

miRNA
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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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SYS1-DBNDD2 expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS <intensity>2/3
CGAP TAG: --
SYS1-DBNDD2 Expression
About this image

SYS1-DBNDD2 Protein expression data from MOPED1, PaxDb2 and MaxQB3 --
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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 animals.

Orthologs for SYS1-DBNDD2 gene from Selected species (see all 8)    About this table
Organism Taxonomic
classification
Gene Description Human
Similarity
Orthology
Type
Details
chicken
(Gallus gallus)
Aves SYS16
Gallus gallus SYS1 Golgi-localized integral membra...
36(a)
1 → many
20(5464904-5467153)
lizard
(Anolis carolinensis)
Reptilia --
Uncharacterized protein
42(a)
1 → many
GL343291.1(1681253-1693017)
zebrafish
(Danio rerio)
Actinopterygii sys16
SYS1 Golgi-localized integral membrane protein hom...
39(a)
1 → many
6(54393140-54400087) ENSDARG00000017606
fruit fly
(Drosophila melanogaster)
Insecta CG117536
--
20(a)
1 → many
3R(4478738-4479569)
worm
(Caenorhabditis elegans)
Secernentea T03F1.126
Protein T03F1.12 (T03F1.12) mRNA, complete cds
14(a)
1 → many
I(3876043-3876704) WBGene00020193
        Species with no ortholog for SYS1-DBNDD2

ENSEMBL Gene Tree for SYS1-DBNDD2 (if available)
TreeFam Gene Tree for SYS1-DBNDD2 (if available)

(Paralogs according to 1HomoloGene,
2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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Paralogs for SYS1-DBNDD2 gene
SYS12  
1 SIMAP similar gene for SYS1-DBNDD2 using alignment to 2 protein entries:     F2Z2A3_HUMAN (see all proteins):
SYS1

SYS1-DBNDD2 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), 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 SYS1-DBNDD2 (see all 498)    About this table    
Genomic DataTranscription Related DataAllele Frequencies
SNP IDValidClinical
significance
Chr 20 posSequence#AA
Chg
TypeMore#Allele
freq
PopTotal
sample
More
----------
rs1451686791,2
--44008998(+) TTCTCA/GCATAT 1 -- int10--------
rs27416361,2
H--44009015(-) AATAAG/AAAAGG 1 -- int14Minor allele frequency- A:0.00NS EA 414
rs1853452241,2
--44009170(+) ACATAC/TCCCTC 1 -- int10--------
rs27416311,2
H--44009318(-) GCCTAG/ACACAC 1 -- int14Minor allele frequency- A:0.00NS EA 418
rs27416301,2
H--44009364(-) GTGAAC/ATCAGA 1 -- int14Minor allele frequency- A:0.00NS EA 416
rs1421923171,2
--44009369(+) GTTCAC/TAGGCC 1 -- int10--------
rs73608271,2
H--44009371(+) TCACAG/AGCCAA 1 -- int14Minor allele frequency- A:0.00NS EA 420
rs1888287421,2
--44009428(+) TGTCCA/GTTTTA 1 -- int10--------
rs1819042301,2
--44009445(+) GATAAG/TCCACC 1 -- int10--------
rs27434401,2
H--44009566(+) ggagcC/Ttccca 1 -- int14Minor allele frequency- T:0.00NS EA 420

HapMap Linkage Disequilibrium report for SYS1-DBNDD2 (43991809 - 44039250 bp)

Structural Variations
      Database of Genomic Variants (DGV) variations for SYS1-DBNDD2: --
Site Specific Mutation Identification with PCR Assays
Search QIAGEN SeqTarget long-range PCR primers for resequencing SYS1-DBNDD2
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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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(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 SYS1-DBNDD2 gene integrated from 10 sources:
(articles sorted by number of sources associating them with SYS1-DBNDD2)
    Utopia: connect your pdf to the dynamic
world of online information

  1. Expression of conjoined genes: another mechanism for gene regulation in eukaryotes. (PubMed id 20967262)1 Prakash T....Taylor T.D. (PLoS ONE 2010)
  2. 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)
  3. The sequence of the human genome. (PubMed id 11181995)1 Venter J.C.... Zhu X. (Science 2001)

(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: 767557 HGNC: 33535 Ensembl:ENSG00000254806 euGenes: HUgn767557 ECgene: SYS1-DBNDD2
H-InvDB: SYS1-DBNDD2

(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 SYS1-DBNDD2 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 SYS1-DBNDD2 gene:
Search GeneIP for patents involving SYS1-DBNDD2

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, Gene Editing from DNA2.0. Clones from OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Cell lines from GenScript, and ESI BIO, 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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