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FAM27L Gene

RNA gene   GIFtS: 31
GCID: GC17P021825

Family With Sequence Similarity 27-Like

  See FAM27L-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)
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Subcategory (RNA class): lncRNA

Quality score for this RNA gene is 3

Aliases
Family With Sequence Similarity 27-Like1 2

External Ids:    HGNC: 324101   Entrez Gene: 2841232   Ensembl: ENSG000001781307   UniProtKB: Q8N5T83   
ORGUL members:         

Export aliases for FAM27L gene to outside databases

Previous GC identifers: GC17P021750 GC17P021026


(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 FAM27L Gene:
FAM27L (family with sequence similarity 27-like) is an RNA gene, and is affiliated with the lncRNA class. Diseases associated with FAM27L include chronic myeloid leukemia.


(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_000017.10  NC_018928.2  NT_024862.15  
Regulatory elements:
   Regulatory transcription factor binding sites in the FAM27L gene promoter:
         AP-1   GCNF   HNF-1A   POU2F1   GCNF-1   HNF-1   POU2F1a   GCNF-2   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidFAM27L promoter sequence
   Search Chromatin IP Primers for FAM27L

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat FAM27L


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

Entrez Gene cytogenetic band: 17p11.2   Ensembl cytogenetic band:  17p11.2   HGNC cytogenetic band: 17p11.2

FAM27L Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
FAM27L gene location

GeneLoc information about chromosome 17         GeneLoc Exon Structure

GeneLoc location for GC17P021825:  view genomic region     (about GC identifiers)

Start:
21,825,297 bp from pter      End:
21,826,499 bp from pter
Size:
1,203 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, Cloud-Clone Corp., and/or eBioscience,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, Cloud-Clone Corp., and/or eBioscience, 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: FA27L_HUMAN, Q8N5T8 (See protein sequence)
Recommended Name: Protein FAM27L  
Size: 71 amino acids; 8147 Da

Explore the universe of human proteins at neXtProt for FAM27L: NX_Q8N5T8


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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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ProtoNet protein and cluster: Q8N5T8

UniProtKB/Swiss-Prot: FA27L_HUMAN, Q8N5T8
Similarity: Belongs to the FAM27 family


(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, 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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Subcellular locations from COMPARTMENTS: 

CompartmentConfidence
cytosol2
nucleus2
extracellular1
mitochondrion1

(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 FAM27L
Interactions:

    Search GeneGlobe Interaction Network for FAM27L

(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 FAM27L (FA27L)



(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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REFSEQ mRNAs for FAM27L gene: 
NM_203392.2  

Unigene Cluster for FAM27L:

Family with sequence similarity 27-like
Hs.348578
Unigene Representative Sequence: BC031617
1 Ensembl transcript including schematic representation, and UCSC links where relevant:
ENST00000426869(lincRNA)(uc002gyz.3)
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Additional mRNA sequence: 

BC031617.1 NR_028336.1 

1 DOTS entry:

DT.95304591 

3 AceView cDNA sequences:

BC031617 BI827418 NM_203392 

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 FAM27L:none

FAM27L expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS <intensity>2/3
CGAP TAG: GTGGCCTCTC
FAM27L Expression
About this image

FAM27L Protein expression data from MOPED1, PaxDb2 and MaxQB3 --

SOURCE GeneReport for Unigene cluster: Hs.348578
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In Situ
Assay Products:
 

 
Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for FAM27L

(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 FAM27L (if available)
TreeFam Gene Tree for FAM27L (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 FAM27L (see all 84)    About this table                                 

Genomic DataTranscription Related DataAllele Frequencies
SNP IDValidClinical
significance
Chr 17 posSequence#AA
Chg
TypeMore#Allele
freq
PopTotal
sample
More
----------
rs1476533811,2
--21823743(+) CCTAAC/TGGATT 1 -- us2k10--------
rs2019901691,2
--21823996(+) AAAAT-/ATCATTTT 1 -- us2k10--------
rs1477887831,2
C--21824388(+) CTTTAC/TGTGTA 1 -- us2k10--------
rs1502850761,2
--21824417(+) TAATCA/GTATTC 1 -- us2k10--------
rs1448987491,2
C--21824571(+) GACCTA/CTGTGG 1 -- us2k10--------
rs1451619721,2
--21824576(+) CTGTGG/TCCGGA 1 -- us2k10--------
rs1834525451,2
--21824597(+) TCACCA/GGGTTT 1 -- us2k10--------
rs576325111,2
--21825081(+) GATACA/GATGGC 1 -- us2k10--------
rs1506631081,2
C--21825109(+) GCCAGC/TCACTC 1 -- us2k10--------
rs1866371031,2
--21825158(+) TCTCCC/TACGCC 1 -- us2k10--------

HapMap Linkage Disequilibrium report for FAM27L (21825297 - 21826499 bp)

Structural Variations
     Database of Genomic Variants (DGV) Selected variations for FAM27L (see all 30):    About this table    
Variant IDTypeSubtypePubMed ID
esv2660756CNV Deletion23128226
dgv539e199CNV Deletion23128226
dgv3116n71CNV Loss21882294
nsv457715CNV Loss19166990
nsv833404CNV Loss17160897
nsv833402CNV Loss17160897
nsv470584CNV Gain18288195
dgv3117n71CNV Gain21882294
dgv3122n71CNV Gain21882294
dgv3121n71CNV Gain21882294

Human Gene Mutation Database (HGMD): FAM27L
Site Specific Mutation Identification with PCR Assays
Search QIAGEN SeqTarget long-range PCR primers for resequencing FAM27L
DNA2.0 Custom Variant and Variant Library Synthesis for FAM27L

(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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1 disease for FAM27L:    
About MalaCards
chronic myeloid leukemia


Find genes that share disorders with FAM27L           About GenesLikeMe


Export disorders for FAM27L 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 FAM27L gene integrated from 10 sources:
(articles sorted by number of sources associating them with FAM27L)
    Utopia: connect your pdf to the dynamic
world of online information

  1. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)1, 2 Gerhard D.S.... Malek J. (Genome Res. 2004)
  2. A genome-wide association study identifies novel loci associated with susceptibility to chronic myeloid leukemia. (PubMed id 21540461)1 Kim D.H....Lipton J.H. (Blood 2011)
  3. 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)

(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: 284123 HGNC: 32410 AceView: LOC284123 Ensembl:ENSG00000178130 euGenes: HUgn284123
ECgene: FAM27L H-InvDB: FAM27L

(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 FAM27L 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 FAM27L gene:
Search GeneIP for patents involving FAM27L

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, eBioscience, and/or others, Gene Editing from DNA2.0. Clones from OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Addgene, Cell lines from GenScript, and ESI BIO, Flow cytometery from eBioscience, 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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