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FAM201A Gene

RNA gene   GIFtS: 27
GCID: GC09P038620

Family With Sequence Similarity 201, Member A

(Previous name: chromosome 9 open reading frame 122)
(Previous symbol: C9orf122)
  Search for FAM201A
at  

(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): lncRNA

Quality score for this RNA gene is 3

Aliases
Family With Sequence Similarity 201, Member A1 2
C9orf1221 2 3
Chromosome 9 Open Reading Frame 1221

External Ids:    HGNC: 272391   Entrez Gene: 1582282   Ensembl: ENSG000002048607   UniProtKB: Q5SY853   
ORGUL members:         

Export aliases for FAM201A 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 FAM201A Gene:
FAM201A (family with sequence similarity 201, member A) is an RNA gene, and is affiliated with the lncRNA class.


(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:
NC_000009.12  NC_018920.2  NT_008413.19  
Regulatory elements:
   Search for regulatory transcription factor binding sites for FAM201A
         Other transcription factors

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Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat FAM201A


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

Entrez Gene cytogenetic band: 9p13.1   Ensembl cytogenetic band:  9p13.1   HGNC cytogenetic band: 9p12

FAM201A Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
FAM201A gene location

GeneLoc information about chromosome 9         GeneLoc Exon Structure

GeneLoc location for GC09P038620:  view genomic region     (about GC identifiers)

Start:
38,620,471 bp from pter      End:
38,624,987 bp from pter
Size:
4,517 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/Swiss-Prot: F201A_HUMAN, Q5SY85 (See protein sequence)
Recommended Name: Protein FAM201A  
Size: 155 amino acids; 16478 Da

Explore the universe of human proteins at neXtProt for FAM201A: NX_Q5SY85

Explore proteomics data for FAM201A at MOPED


See FAM201A Protein Expression from SPIRE MOPED, PaxDB, and MaxQB


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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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HGNC Gene Families:
LNCRNA: Long non-coding RNAs

ProtoNet protein and cluster: Q5SY85


(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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Subcellular locations from COMPARTMENTS: 

CompartmentConfidence
extracellular2
cytosol1
mitochondrion1
nucleus1

(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 FAM201A
Interactions:

    Search GeneGlobe Interaction Network for FAM201A

(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
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Browse Tocris compounds for FAM201A (F201A)



(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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Unigene Cluster for FAM201A:

Family with sequence similarity 201, member A
Hs.632652  [show with all ESTs]
Unigene Representative Sequence: BC036230
3 Ensembl transcripts including schematic representations, and UCSC links where relevant:
ENST00000471864(antisense) ENST00000484285(antisense) ENST00000377680(antisense)
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Additional mRNA sequence: 

BC036230.1 BC041970.1 BC067887.1 NR_027294.1 

4 DOTS entries:

DT.95095613  DT.91950532  DT.95195806  DT.97778179 

10 AceView cDNA sequences:

BC041970 BM925292 AW665228 BI602107 BC067887 AI681160 BC036230 BI597167 
BI765151 BG701504 

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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Expression evidence for FAM201A:none

FAM201A expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS <intensity>2/3
CGAP TAG: GTAGAAATTT
FAM201A Expression
About this image

FAM201A Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

FAM201A Protein Expression

SOURCE GeneReport for Unigene cluster: Hs.632652
    Custom PCR Arrays for FAM201A
Primer
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In Situ
Assay Products:
 

 
Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for FAM201A

(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 FAM201A (if available)
TreeFam Gene Tree for FAM201A (if available)

(Paralogs according to 1HomoloGene,
2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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Paralogs for FAM201A gene

FAM201A for paralogs           About GeneDecksing


Selected Pseudogenes.org Pseudogenes for FAM201A (see all 24)
PGOHUM00000246964 PGOHUM00000247006 PGOHUM00000244896 PGOHUM00000244897 PGOHUM00000238985


(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 FAM201A (see all 20)    About this table    
Genomic DataTranscription Related DataAllele Frequencies
SNP IDValidClinical
significance
Chr 9 posSequence#AA
Chg
TypeMore#Allele
freq
PopTotal
sample
More
----------
rs1827794871,2
--38622821(+) TGCCAC/GACAGG 1 -- nc-transcript-variant0--------
rs797647971,2
C,F--38622931(+) TCTTCT/CTTCAT 1 -- nc-transcript-variant1Minor allele frequency- C:0.02NA 120
rs1877617911,2
--38623043(+) ACAGCG/TTTTGG 1 -- nc-transcript-variant0--------
rs1930188361,2
--38623077(+) GAATTA/CATAAA 1 -- nc-transcript-variant0--------
rs2003917151,2
C--38623116(-) GCAACA/CCAGCC 1 -- nc-transcript-variant0--------
rs1856449771,2
--38623149(+) TTCACA/GGATGC 1 -- nc-transcript-variant0--------
rs1877716351,2
--38623172(+) AAACCA/GGAGAA 1 -- nc-transcript-variant0--------
rs1926427681,2
--38623361(+) TCGCTC/TTTTCG 1 -- int10--------
rs1445585461,2
--38623395(+) GGTCTC/TGGCTC 1 -- int10--------
rs1137499951,2
F--38623527(+) TTGTGG/ATTTGA 1 -- int11Minor allele frequency- A:0.50CSA 2

HapMap Linkage Disequilibrium report for FAM201A (38620471 - 38624987 bp)

Structural Variations
     Database of Genomic Variants (DGV) 5 variations for FAM201A:    About this table    
Variant IDTypeSubtypePubMed ID
esv27275CNV Loss19812545
dgv261e55CNV Loss17911159
nsv8445CNV Gain+Loss18304495
dgv2313e1CNV Complex17122850
dgv2312e1CNV Complex17122850

Site Specific Mutation Identification with PCR Assays
SeqTarget long-range PCR primers for resequencing FAM201A
DNA2.0 Custom Variant and Variant Library Synthesis for FAM201A

(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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FAM201A for disorders           About GeneDecksing

Genetic Association Database (GAD): FAM201A

Export disorders for FAM201A 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 FAM201A gene integrated from 10 sources:
(articles sorted by number of sources associating them with FAM201A)
    Utopia: connect your pdf to the dynamic
world of online information

  1. DNA sequence and analysis of human chromosome 9. (PubMed id 15164053)1, 2 Humphray S.J.... Dunham I. (Nature 2004)
  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. (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: 158228 HGNC: 27239 AceView: C9orf122 Ensembl:ENSG00000204860 euGenes: HUgn158228
ECgene: FAM201A H-InvDB: FAM201A

(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 FAM201A 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 FAM201A gene:
Search GeneIP for patents involving FAM201A

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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