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

ZFAS1 Gene

RNA gene   GIFtS: 23
GCID: GC20P047910

ZNFX1 Antisense RNA 1

(Previous names: chromosome 20 open reading frame 199, non-protein coding...)
(Previous symbols: C20orf199, NCRNA00275, ZNFX1-AS1)
  See related diseases
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

Subcategory (RNA class): lncRNA

Quality score for this RNA gene is 4

Aliases
ZNFX1 Antisense RNA 11 2     Non-Protein Coding RNA 2751
C20orf1991 2     ZNFX1 Antisense RNA 1 (Non-Protein Coding)1
NCRNA002751 2     HSUP12
ZNFX1-AS11 2     HSUP22
Chromosome 20 Open Reading Frame 1991     

External Ids:    HGNC: 331011   Entrez Gene: 4419512   Ensembl: ENSG000001774107   
ORGUL members:         
NONCODE14:n378874 n383929 n379101 n377667 n406183 see all 11      
Rfam:RF02215    

Export aliases for ZFAS1 gene to outside databases

Previous GC identifer: GC20P047905


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

GeneCards Summary for ZFAS1 Gene: 
ZFAS1 (ZNFX1 antisense RNA 1) is an RNA gene, and is affiliated with the lncRNA class. Diseases associated with ZFAS1 include intrahepatic cholangiocarcinoma, and cholangiocarcinoma.


(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  NC_018931.2  NT_011362.10  
Regulatory elements:
   Search SABiosciences Regulatory transcription factor binding sites for ZFAS1
         Other transcription factors

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Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat ZFAS1


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

Entrez Gene cytogenetic band: 20q13.13   Ensembl cytogenetic band:  20q13.13   HGNC cytogenetic band: 20q13.13

ZFAS1 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
ZFAS1 gene location

GeneLoc information about chromosome 20         GeneLoc Exon Structure

GeneLoc location for GC20P047910:  view genomic region     (about GC identifiers)

Start:
47,894,715 bp from pter      End:
47,905,797 bp from pter
Size:
11,083 bases      Orientation:
plus strand
ORGUL member locations:
Legend (see complete legend)

ORGUL Member Locations for ZFAS1

(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: --


(According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
About This Section
HGNC Gene Families: 
LNCRNA: Long non-coding RNAs

  --

(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

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 ZFAS1

(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
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Browse Tocris compounds for ZFAS1

Search CenterWatch for drugs/clinical trials and news about ZFAS1

(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

Unigene Cluster for ZFAS1:

ZNFX1 antisense RNA 1
Hs.356766  [show with all ESTs]
Unigene Representative Sequence: CR936805
7 Ensembl transcripts including schematic representations, and UCSC links where relevant:
ENST00000371743(uc002xul.4 uc002xuj.3) ENST00000441722(uc002xum.4)
ENST00000417721(uc002xun.4) ENST00000450535 ENST00000458653 ENST00000326677(uc002xuo.3)
ENST00000428008
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Additional mRNA sequence: 

AK124175.1 AY339614.1 BC032480.1 BC042807.1 BC060315.1 BC062222.1 BC062447.1 BC105282.1 
CR749730.1 CR936805.1 NR_003604.2 NR_003605.1 NR_003606.2 NR_036658.1 NR_036659.1 

24/30 DOTS entries (see all 30):

DT.100886287  DT.95303736  DT.456371  DT.99981129  DT.120795621  DT.95152227  DT.95174022  DT.99935865 
DT.100886294  DT.101985148  DT.100059585  DT.97784074  DT.92445366  DT.97814763  DT.100886292  DT.75159797 
DT.120795543  DT.100886297  DT.99953564  DT.120795721  DT.92015551  DT.95259841  DT.95279889  DT.120795738 

24/498 AceView cDNA sequences (see all 498):

T33971 AA740573 CD676408 AI364930 BU736940 BF197666 AI056717 D19835 
CD674657 AI056087 AI889031 BM785489 AA316900 AI820039 AI263001 CB140008 
W73570 AI092185 BE897330 AA960813 CD678954 CA450260 AA461309 T34373 

GeneLoc Exon Structure

5/9 Alternative Splicing Database (ASD) splice patterns (SP) for ZFAS1 (see all 9)    About this scheme

ExUns: 1 ^ 2a · 2b · 2c ^ 3a · 3b ^ 4 ^ 5 ^ 6 ^ 7 ^ 8
SP1:                    -           -                       -         
SP2:                    -           -                 -               
SP3:        -     -     -           -                 -     -         
SP4:                    -           -                 -     -         
SP5:                                -                 -     -         


ECgene alternative splicing isoforms for ZFAS1

(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

Expression evidence for ZFAS1:none

See probesets specificity/sensitivity at GeneAnnot
CGAP TAG: --


Genevestigator expression for ZFAS1

SOURCE GeneReport for Unigene cluster: Hs.356766
    SABiosciences Custom PCR Arrays for ZFAS1
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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
  --

ENSEMBL Gene Tree for ZFAS1 (if available)
TreeFam Gene Tree for ZFAS1 (if available)

(Paralogs according to 1HomoloGene,
2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
About This Section
  --

(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

10/251 SNPs in ZFAS1 are shown (see all 251)    About this table     
Genomic DataTranscription Related DataAllele Frequencies
SNP IDValidClinical
significance
Chr 20 posSequence#AA
Chg
TypeMore#Allele
freq
PopTotal
sample
More
----------
rs1827088391,2
--47897839(+) TGGCTG/TGAGTC 5 -- int10--------
rs768454591,2
--47897975(+) ATAGGA/GAACAG 5 -- int10--------
rs1429827741,2
C--47898002(+) GCCGG-/AGAAGTT
GTTTATAGA
AGAAG
5 -- int10--------
rs1866308371,2
--47898029(+) TAACTC/TGGAGC 5 -- int10--------
rs795700091,2
C,F--47898038(+) GCAGGA/GAGGTA 5 -- int11Minor allele frequency- G:0.10EA 120
rs1898129461,2
C--47898047(+) TATGAA/GGAAGT 5 -- int10--------
rs1455627011,2
C--47898060(+) ACCTT-/AA    
   GAACA
AAGAA
5 -- int10--------
rs1826448351,2
--47898102(+) AATCCA/GTTGTA 5 -- int10--------
rs766199871,2
--47898145(+) TATTTA/CTCTTC 5 -- int10--------
rs771167941,2
C,F--47898148(+) TTCTCT/CTCAGA 5 -- int11Minor allele frequency- C:0.01WA 118

HapMap Linkage Disequilibrium report for ZFAS1 (47894715 - 47905797 bp)

Structural Variations
      Database of Genomic Variants (DGV) variations for ZFAS1: --
SABiosciences Cancer Mutation PCR Assays
Search QIAGEN SeqTarget long-range PCR primers for resequencing ZFAS1
DNA2.0 Custom Variant and Variant Library Synthesis for ZFAS1

(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
4 diseases for ZFAS1:    About MalaCards
intrahepatic cholangiocarcinoma    cholangiocarcinoma    gastric cancer    breast cancer


ZFAS1 for disorders           About GeneDecksing


Export disorders for ZFAS1 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 ZFAS1 gene integrated from 9 sources:
(articles sorted by number of sources associating them with ZFAS1)
    Utopia: connect your pdf to the dynamic
world of online information

  1. SNORD-host RNA Zfas1 is a regulator of mammary develo pment and a potential marker for breast cancer. (PubMed id 21460236)1, 3 Askarian-Amiri M.E....Mattick J.S. (2011)
  2. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. (PubMed id 12477932)1, 3 Strausberg R.L....Marra M.A. (2002)
  3. Hundreds of variants clustered in genomic loci and bi ological pathways affect human height. (PubMed id 20881960)1 Lango Allen H....Hirschhorn J.N. (2010)
  4. Identification of intrahepatic cholangiocarcinoma related genes by comparison with normal liver tissues using expressed sequence tags. (PubMed id 16712791)1 Wang A.G....Kim N.S. (2006)
  5. Transcriptome analysis of human gastric cancer. (PubMed id 16341674)1 Oh J.H....Kim N.S. (2005)
  6. The DNA sequence and comparative analysis of human chromosome 20. (PubMed id 11780052)1 Deloukas P....Rogers J. (2001)
  7. Normalization and subtraction: two approaches to facilitate gene discovery. (PubMed id 8889548)1 Bonaldo M.F.... Soares M.B. (1996)

(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: 441951 HGNC: 33101 AceView: LOC441951 Ensembl:ENSG00000177410 euGenes: HUgn441951
ECgene: ZFAS1 H-InvDB: ZFAS1

(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 ZFAS1 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 ZFAS1 gene:
Search GeneIP for patents involving ZFAS1

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: 3 Nov 2013 , 7 Nov 2013 , 23 Jan 2014

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