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ZFAS1 Gene

RNA gene   GIFtS: 22
GCID: GC20P047917

ZNFX1 Antisense RNA 1

(Previous names: chromosome 20 open reading frame 199, non-protein coding...)
(Previous symbols: C20orf199, NCRNA00275, ZNFX1-AS1)
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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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Subcategory (RNA class): antisense

Quality score for this RNA gene is 5.2

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:    fRNAdb10:FR144492 FR407497      
H-InvDB12:HIT000385901    
NCBI13:AM413026    
NONCODE14:n378874 n383929 n379101 n406183 n377959 see all 9    
Rfam:RF02215    
RNAdb15:RNZ21573    

Export aliases for ZFAS1 gene to outside databases

Previous GC identifers: GC20P047905 GC20P047910


(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 ZFAS1 Gene:
ZFAS1 (ZNFX1 antisense RNA 1) is an RNA gene, and is affiliated with the antisense RNA class.

fRNAdb sequence ontologies for ZFAS1 - the ORGUL cluster for this gene includes several descriptions:
-
nc_conserved_region - Non-coding region of sequence similarity by descent from a common ancestor.
ncRNA - An RNA transcript that does not encode for a protein rather the RNA molecule is the gene product.

View fRNAdb secondary structures for ZFAS1

(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_000020.10  NC_018931.2  NT_011362.11  
Regulatory elements:
   Search for regulatory transcription factor binding sites for ZFAS1
         Other transcription factors

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Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing 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 GC20P047917:  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 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., eBioscience, and/or antibodies-online,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, Cloud-Clone Corp., eBioscience, and/or antibodies-online, Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, Abcam, Cloud-Clone Corp, antibodies-online, and/or others.)
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UniProtKB: --


(According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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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, 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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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 ZFAS1
Interactions:

    Search GeneGlobe Interaction Network for ZFAS1

(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
  Browse compounds at ApexBio 

Browse Tocris compounds for 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,
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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2 fRNAdb Secondary structures:


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(antisense) ENST00000441722(antisense) ENST00000417721(antisense) ENST00000450535(antisense) ENST00000458653(antisense)
ENST00000326677(antisense) ENST00000428008(antisense)
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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 

Selected 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 

Selected AceView cDNA sequences (see all 498):

BM876277 AA316900 CB137861 AA740573 BQ018444 W73570 T34372 AI364930 
N79545 BU076411 AI734997 AA960813 AI056087 BU736940 BU071337 AI089410 
AI597603 BF197666 CB137126 CB138604 AI344550 AI263001 CB138600 T35907 

GeneLoc Exon Structure

Selected 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™, 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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Expression evidence for ZFAS1:H-invDB

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

ZFAS1 Protein expression data from MOPED1, PaxDb2 and MaxQB3 --

SOURCE GeneReport for Unigene cluster: Hs.356766
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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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  --

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)
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  --

(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 ZFAS1 (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: --
Site Specific Mutation Identification with 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, 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 ZFAS1 gene, integrated from 10 sources (see all 11):
(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 development and a potential marker for breast cancer. (PubMed id 21460236)1, 3 Askarian-Amiri M.E....Mattick J.S. (RNA 2011)
  2. Hundreds of variants clustered in genomic loci and biological pathways affect human height. (PubMed id 20881960)1 Lango Allen H....Hirschhorn J.N. (Nature 2010)
  3. 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. (Biochem. Biophys. Res. Commun. 2006)
  4. Transcriptome analysis of human gastric cancer. (PubMed id 16341674)1 Oh J.H.... Kim N.S. (Mamm. Genome 2005)
  5. 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)
  6. The DNA sequence and comparative analysis of human chromosome 20. (PubMed id 11780052)1 Deloukas P....Rogers J. (Nature 2001)
  7. Normalization and subtraction: two approaches to facilitate gene discovery. (PubMed id 8889548)1 Bonaldo M.F.... Soares M.B. (Genome Res. 1996)
  8. (PubMed id 16273071)10 
  9. (PubMed id 15608161)10 
  10. (PubMed id 18089548)10 

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

(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 ZFAS1 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 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



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