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CHRFAM7A Gene

protein-coding   GIFtS: 49

GC15M030653
CHRNA7 (cholinergic receptor, nicotinic, alpha 7, exons 5-10) and FAM7A (family with sequence similarity 7A, exons A-E) fusion
Symbol approved by the HUGO Gene Nomenclature Committee (HGNC) database
Products    

Aliases &
Descriptions
for CHRFAM7A gene

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc , and/or 7Ensembl, 8miRBase)
About This Section
Aliases & Descriptions
CHRNA7 (cholinergic receptor, nicotinic, alpha 7, exons 5-10) and FAM7A (family
with sequence similarity 7A, exons A-E) fusion1 2
     alpha 7 neuronal nicotinic acetylcholine receptor-FAM7A hybrid2
D-101 2 3     CHRNA72
CHRNA7-DR11 2 3     CHRNA7 (cholinergic receptor, nicotinic, alpha polypeptide 7, exons 5-10) and
FAM7A (family with sequence similarity 7A, exons A-E) fusion2
MGC1204822     MGC1204832
CHRNA7-FAM7A fusion protein2     alpha-7 nicotinic cholinergic receptor subunit2

External Ids:    HGNC: 157811   Entrez Gene: 898322   Ensembl: ENSG000001666647   UniProtKB: Q494W83   

Export aliases for CHRFAM7A gene to outside databases

Previous GC identifers: GC15M025924 GC15M023461 GC15M028233 GC15M028369 GC15M028440


Summaries
for CHRFAM7A gene

(According to Entrez Gene, Tocris Bioscience, Wikipedia's Gene Wiki,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
About This Section
Entrez Gene summary for CHRFAM7A:
The nicotinic acetylcholine receptors (nAChRs) are members of a superfamily of ligand-gated ion channels that mediate
fast signal transmission at synapses. The family member CHRNA7, which is located on chromosome 15 in a region
associated with several neuropsychiatric disorders, is partially duplicated and forms a hybrid with a novel gene from
the family with sequence similarity 7 (FAM7A). Alternative splicing has been observed, and two variants exist, for
this hybrid gene. The N-terminally truncated products predicted by the largest open reading frames for each variant
would lack the majority of the neurotransmitter-gated ion-channel ligand binding domain but retain the transmembrane
region that forms the ion channel. Although current evidence supports transcription of this hybrid gene, translation
of the nicotinic acetylcholine receptor-like protein-encoding open reading frames has not been confirmed. (provided by
RefSeq)

Gene Wiki entry for CHRFAM7A

Genomic Views
for CHRFAM7A gene

(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 60), Regulatory elements and Epigenetics data according to Qiagen and/or SABiosciences)
About This Section
Regulatory elements:
   SABiosciences Regulatory transcription factor binding sites in the CHRFAM7A gene promoter:
         p300   p53   RREB-1   POU2F1   NRSF form 1   NRSF form 2   SRF   Meis-1   HOXA9B   STAT5B   
         Other transcription factors

   Search SABiosciences Chromatin IP Primers for CHRFAM7A

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays 


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

Entrez Gene cytogenetic band: 15q13.1   Ensembl cytogenetic band:  15q13.2   HGNC cytogenetic band: 15q13.1

CHRFAM7A Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
CHRFAM7A gene location

GeneLoc gene densities for chromosome 15         GeneLoc Exon Structure

GeneLoc location for GC15M030653:  view genomic region     (about GC identifiers)

Start:
 30,653,443 bp from pter
End:
 30,685,864 bp from pter
Size:
 32,422 bases
Orientation:
 minus strand
RefSeq DNA sequence:
NC_000015.9  NT_010194.17  

Proteins
for CHRFAM7A gene

(According to 1UniProtKB, neXtProt, and/or Ensembl, Phosphorylation sites according to 2Phosphosite, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from Millipore, Sigma-Aldrich, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, and/or ProSpec,
Biochemical Assays by Millipore, Sigma-Aldrich, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Uscn, Ontologies according to Gene Ontology Consortium 01 Dec 2010 and Entrez Gene, Antibodies by Millipore, Sigma-Aldrich, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, and/or Epitomics)
About This Section
UniProtKB/Swiss-Prot: CRFM7_HUMAN, Q494W8 (See protein sequence)
Recommended Name: CHRNA7-FAM7A fusion protein  
Size: 412 amino acids; 46218 Da
Subcellular location: Membrane; Multi-pass membrane protein (By similarity)
Caution: This protein is encoded by a hybrid gene consisting of a duplication of exons 5 through 10 of the CHRNA7 gene
fused 3-prime to a copy of the FAM7A gene (exons A through E). The CHRFAM7A gene is in the opposite orientation to the
CHRNA7 gene. It seems not to be represented on every human chromosome 15 and it is not clear whether the transcript is
actually translated
Secondary accessions: A8KAB9

Explore the universe of human proteins at neXtProt for CHRFAM7A: NX_Q494W8 

REFSEQ proteins (2 alternative transcripts): 
NP_647536.1  NP_683709.1  


ENSEMBL proteins: 
ENSP00000380927 ENSP00000299847 ENSP00000385389 


Human Recombinant Proteins 
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3 Gene Ontology (GO) cellular component terms (GO ID links to tree view):

GO IDQualified GO termEvidencePubMed IDs
GO:0016020 membrane ----
GO:0016021 integral to membrane IEA--
GO:0045211 postsynaptic membrane IEA--
About this table

CHRFAM7A for ontologies           About GeneDecksing



Antibodies for CHRFAM7A: 
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Protein Domains/
Families
for CHRFAM7A gene

(According to InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
About This Section
CHRFAM7A for domains           About GeneDecksing

4 InterPro domains/families:
 IPR018000 Neurotransmitter_ion_chnl_CS
 IPR006201 Neur_channel
 IPR006202 Neur_chan_lig-bd
 IPR006029 Neurotrans-gated_channel_TM

Graphical View of Domain Structure for InterPro Entry Q494W8

ProtoNet protein and cluster: Q494W8

UniProtKB/Swiss-Prot: CRFM7_HUMAN, Q494W8
Similarity: Belongs to the ligand-gated ion channel (TC 1.A.9) family


Gene Function
for CHRFAM7A gene

(According to UniProtKB, IUBMB,and/or Genatlas, Animal models from MGI Dec 24 2010,
shRNA from OriGene, Sigma-Aldrich, RNAi from Millipore, siRNAs from Sigma-Aldrich, OriGene, Qiagen, Super-pooled esiRNAs from Sigma-Aldrich, microRNA from Sigma-Aldrich, Qiagen, SABiosciences, Clones from Millipore, Sigma-Aldrich, OriGene, GenScript, Sino Biological, Cell Lines from GenScript, Ontologies according to Gene Ontology Consortium 01 Dec 2010 via Entrez Gene.)
About This Section
Inhib.
RNA:    		Browse for Gene Knock-down Tools from Millipore
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QIAGEN FlexiTube/FlexiPlate siRNA for gene silencing of CHRFAM7A 
miRNA:Browse microRNA Mimics at Sigma-Aldrich
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QIAGEN Custom miScript Target Protector blocks miRNA-binding site of CHRFAM7A 
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Gene
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Clones:Browse Clones for the Expression of Recombinant Proteins Available from Millipore
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OriGene GFP tagged cDNA clones in CMV expression vector (see all 2): CHRFAM7A
OriGene Myc/DDK tagged cDNA clones in CMV expression vector (see all 2): CHRFAM7A
OriGene untagged cDNA clones in CMV expression vector (see all 2): CHRFAM7A
OriGene 3'-UTR clone (see all 2): CHRFAM7A 
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Cell
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1 Gene Ontology (GO) molecular function term (GO ID links to tree view):

GO IDQualified GO termEvidencePubMed IDs
GO:0005230 extracellular ligand-gated ion channel activity IEA--
About this table

CHRFAM7A for ontologies           About GeneDecksing


Pathways & Interactions
for CHRFAM7A gene

(Pathways according to Millipore, Cell Signaling Technology, Sigma-Aldrich, KEGG and/or UniProtKB, Sets of similar genes according to GeneDecks, PCR Arrays from SABiosciences, Proteins Network according to SABiosciences, Sigma-Aldrich, Interactions according to 1UniProtKB, 2MINT, and/or 3STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Dec 2010 via Entrez Gene).
About This Section


CHRFAM7A for pathways           About GeneDecksing

1 Sigma-Aldrich "Your Favorite Gene" (powered by Ingenuity) Pathway for  CHRFAM7A
    Calcium Signaling

    SABiosciences Custom Pathway-Focused PCR Arrays for CHRFAM7A 

    Sigma-Aldrich "Your Favorite Gene" (powered by Ingenuity) Molecular Interaction Network for CHRFAM7A
    Search SABiosciences Gene Network CentralTM Interacting Genes and Proteins Networks for CHRFAM7A

2 Gene Ontology (GO) biological process terms (GO ID links to tree view):

GO IDQualified GO termEvidencePubMed IDs
GO:0006810 transport ----
GO:0006811 ion transport IEA--
About this table

CHRFAM7A for ontologies           About GeneDecksing



Drugs & Compounds
for CHRFAM7A gene

(Chemical Compounds according to UniProtKB, Enzo Life Sciences, Sigma-Aldrich, Tocris Bioscience, and/or Novoseek and Drugs according to Enzo Life Sciences and/or PharmGKB)
About This Section
Browse Small Molecules at Sigma-Aldrich
Browse drugs & compounds from Enzo Life Sciences

Browse Tocris compounds for CHRFAM7A


Transcripts
for CHRFAM7A gene

(GenBank/EMBL/DDBJ Accessions according to
Unigene (Build 228 Homo sapiens; Dec 8 2010) or GenBank,
RefSeq according to Entrez Gene,
DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
non coding RNAs according to RNAdb,
ESTs according to GeneTide,
exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
RNAi Products from Millipore,
siRNAs from Sigma-Aldrich, OriGene, Qiagen, Super-pooled esiRNAs from Sigma-Aldrich,
shRNA from Sigma-Aldrich, OriGene, microRNA from Sigma-Aldrich, Qiagen, SABiosciences,
Tagged/untagged cDNA clones from OriGene, Sigma-Aldrich, GenScript, Primers from OriGene and/or SABiosciences)
About This Section
Inhib.
RNA:     		Browse for Gene Knock-down Tools from Millipore
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Clones: Browse FLAG tag genes at Sigma-Aldrich
OriGene GFP tagged cDNA clones in CMV expression vector (see all 2): CHRFAM7A
OriGene Myc/DDK tagged cDNA clones in CMV expression vector (see all 2): CHRFAM7A
OriGene untagged cDNA clones in CMV expression vector (see all 2): CHRFAM7A
OriGene 3'-UTR Clone (see all 2): CHRFAM7A 
Browse OriGene MicroRNA Expression Plasmids 
GenScript cDNA clones with any tag delivered in your preferred vector (see all 2): CHRFAM7A 
Primers: OriGene genome-wide validated SYBR primer pairs: CHRFAM7A
Browse OriGene validated miRNA SYBR primer pairs 
SABiosciences RT2 qPCR Primer Assay for CHRFAM7A: PPH17678A

REFSEQ mRNAs for CHRFAM7A gene (2 alternative transcripts): 

NM_139320.1  NM_148911.1  

Additional cDNA sequence: 

AF029838.1 AF029839.1 AF036903.1 AF037646.1 AK292984.1 BC101345.1 BC101346.2 BC101347.2 
BC101348.2 CR605947.1 

12 DOTS entries:

DT.100025592  DT.100778391  DT.100778392  DT.121031753  DT.121033464  DT.102842464  DT.91679005  DT.92059623 
DT.100778393  DT.121031746  DT.121033553  DT.97837952 

24/71 AceView cDNA sequences (see all 71):

CR608436 BX282644 BC037571 BM451308 NM_000746 CR594008 BI963064 BX090309 
BF507825 AA639641 AI791902 BU149265 BU680930 CR605947 AA301331 AI208142 
BX422848 AA897701 CR620753 BV198462 BX344807 X70297 BF445820 L25827 

highest scoring ESTs for CHRFAM7A:

BM146340 AF029838 AF029839 NM_139320 NM_148911 W03952 W52861 AI821705 DB081169 DN993189 

Unigene Cluster for CHRFAM7A:

CHRNA7 (cholinergic receptor, nicotinic, alpha 7, exons 5-10) and FAM7A (family with sequence similarity 7A, exons A-E) fusion
Hs.510853  [show with all ESTs]
Unigene Representative Sequence: NM_139320


GeneLoc Exon Structure

3 Ensembl transcripts including schematic representations, and UCSC links where relevant:
ENST00000397827(uc001zdt.1 uc001zdu.1 uc010azn.2 uc001zdv.2)
ENST00000299847 ENST00000401522

Expression
for CHRFAM7A gene

(Experimental results according to 1GeneNote and GNF BioGPS,
probe sets-to-genes annotations according to 2GeneAnnot , 3GeneTide , Sets of similar genes according to GeneDecks, Electronic Northern calculations according to data from UniGene (Build 228 Homo sapiens), SAGE tags according to CGAP, plus additional links to SOURCE, and/or GNF BioGPS, and/or EXPOLDB, and/or UniProtKB,
Primers from OriGene and/or SABiosciences )
About This Section

CHRFAM7A expression in normal and diseased human tissues

1  / 2  / 3

4 probe-sets matching CHRFAM7A gene

Affymetrix
probe-set		 Array  GeneAnnot data GeneNote data GeneTide data
# genes Sensitivity Specificity Correlation Length Gb_Accession Consensus Uniqueness Score Rank
39566_at2, 3 U95-A 2 1.00 0.50 0.99 0.53 X70297 0.40 0.20 0.32 2
70426_at*2, 3 U95-D 1 -- -- 0.55 1.55 AI821705 0.40 1.00 0.76 1
210123_s_at2, 3 U133-A 2 1.00 0.50 -- -- U62436 0.20 0.12 0.17 2
210123_s_at2 U133Plus2 2 1.00 0.50 -- -- -- -- -- -- --
About this table

CHRFAM7A for expression           About GeneDecksing

Data from Genenote  (Publications) and GNF BioGPS
    About these images
CHRFAM7A gene expression
CHRFAM7A gene electronic northern expression
CHRFAM7A gene sage expression
About these images

CGAP SAGE TAG: CACTGGAGTT

SOURCE GeneReport for Unigene cluster: Hs.510853

Expression variation in blood from EXPOLDB for CHRFAM7A

UniProtKB/Swiss-Prot: CRFM7_HUMAN, Q494W8
Tissue specificity: Expressed in hippocampus

Primers: OriGene genome-wide validated SYBR primer pairs: CHRFAM7A
Browse OriGene validated miRNA SYBR primer pairs 
SABiosciences RT2 qPCR Primer Assay for CHRFAM7A: PPH17678A
    SABiosciences Custom PCR Arrays for CHRFAM7A 


Orthologs
for CHRFAM7A gene

(Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD and/or 5MGI Dec 24 2010, with possible further links to Flybase and/or WormBase, Gene Trees according to Ensembl)
About This Section
Orthologs for CHRFAM7A gene from 1 species
Organism Gene Locus Description Human
Similarity		 NCBI accessions
rainbow trout
(Oncorhynchus mykiss)		 BX299163.12   --   -- 80.12(n)  BX299163.1 
About this table        Species with no ortholog for CHRFAM7A

ENSEMBL Gene Tree for CHRFAM7A (if available)

Paralogs
for CHRFAM7A gene

(Paralogs according to 1HomoloGene
and 2Ensembl, Pseudogenes according to 3Pseudogene.org)
About This Section
Paralogs for CHRFAM7A gene
CHRNA72  CHRNA102  CHRNA92  

CHRFAM7A for paralogs           About GeneDecksing



Genomic Variants
for CHRFAM7A gene

(SNPs according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, and UniProtKB, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Resequencing Primers from Qiagen)
About This Section

10/19 NCBI SNPs in CHRFAM7A are shown (see all 19)
Genomic DataTranscription Related DataAllele Frequencies
SNP IDValidChr 15 posSequenceRecsAA
Chg		TypeMoreRecsAllele
freq		PopTotal
sample		More
----------
rs8973821,2
--30668340(+) tgtgtC/Gaggtg 2 -- int10--------
rs25646121,2
C30663796(+) atacaA/Ccattc 2 -- int10--------
rs26046941,2
C30657952(+) ACATCA/CCCATG 2 -- int10--------
rs362344651,2
--30668185(+) GAGTCA/GTGTGG 2 -- int10--------
rs620164821,2
--30669831(+) AGAGTA/GCAGTG 2 -- int10--------
rs666895031,2
--30669781(+) ATATC-/TTTTTT 2 -- int10--------
rs719057201,2
--30668186(+) AGTCG-/ATTGGGT 2 -- int10--------
rs719328151,2
--30668333(+) TGTGT-/TGGTGTG 2 -- int10--------
rs722049711,2
--30667880(+) GTGTG-/TGTC  
        TGGTG 		2 -- int10--------
rs723221731,2
--30668129(+) TGTGT-/AGGTTGA 2 -- int10--------
About this table

HapMap Linkage Disequilibrium images for CHRFAM7A (up to first 250kb)
Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions)
Database of Genomic Variants (DGV): 20 variations for CHRFAM7A
     15/20 CNVs (see all 20): 87571 2186 3955 3074 66758 76886 76887 32014 9262 87574 4886 66759 76888 87573 37842

QIAGEN SeqTarget long-range PCR primers for resequencing CHRFAM7A 

Disorders & Mutations
for CHRFAM7A gene

(in which this Gene is Involved, According to OMIM, UniProtKB, PharmGKB, Genatlas, GeneTests, Blood group antigen gene mutations by BGMUT, LSDB, HGMD, GAD, HuGE Navigator, and/or TGDB.)
About This Section
CHRFAM7A for disorders           About GeneDecksing

OMIM: 609756

Human Gene Mutation Database (HGMD): CHRFAM7A
Human Genome Epidemiology (HuGE) Navigator: CHRFAM7A (8 documents)

Export disorders and mutations for CHRFAM7A gene to outside databases

Medical News
for CHRFAM7A gene

(Possibly Related Articles in Doctor's Guide)
About This Section
   --

Publications
for CHRFAM7A gene

(in PubMed. Associations of this gene to articles via 1Entrez Gene, 2UniProtKB/Swiss-Prot, 3HGNC, 4GAD, 5PharmGKB, 6UniProtKB/TrEMBL, and/or 7Novoseek)
About This Section

10/21 PubMed articles for CHRFAM7A gene, integrated from 7 sources (see all 21):
(articles sorted by number of sources associating them with CHRFAM7A)
  1. Analysis of the DNA sequence and duplication history of human chromosome 15. (PubMed id 16572171)1, 2 Zody M.C....Nusbaum C. (2006)
  2. 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. (2004)
  3. A 3-Mb map of a large segmental duplication overlapping the alpha7- nicotinic acetylcholine receptor gene (CHRNA7) at human 15q13-q14. (PubMed id 11829490)1, 3 Riley B.... Makoff A. (2002)
  4. Genomic organization and partial duplication of the human alpha7 neuronal nicotinic acetylcholine receptor gene (CHRNA7). (PubMed id 9782083)1, 2 Gault J.... Leonard S. (1998)
  5. A 2-base pair deletion polymorphism in the partial du plication of the alpha7 nicotinic acetylcholine gene (CHRFAM7A) on chromosome 1 5q14 is associated with schizophrenia. (PubMed id 19631623)1, 7 Sinkus M.L....Leonard S. (2009)
  6. CHRFAM7A copy number and 2-bp deletion polymorphisms and antisaccade performance. (PubMed id 19149910)1, 7 Petrovsky N....Ettinger U. (2009)
  7. Association study of CHRFAM7A copy number and 2 bp deletion polymorphisms with schizophrenia and bipolar affective disorder. (PubMed id 16823804)1, 7 Flomen R.H....Makoff A.J. (2006)
  8. Smoking in adult attention-deficit/hyperactivity diso rder: Interaction between 15q13 nicotinic genes and Temperament Character Inven tory scores. (PubMed id 19462340)1, 7 Manchia M....Kennedy J.L. (2009)
  9. Poor replication of candidate genes for major depress ive disorder using genome-wide association data. (PubMed id 20351714)1 Bosker F.J....Nolen W.A. (2010)
  10. Association between a genetic variant of the alpha-7 nicotinic acetylcholine receptor subunit and four types of dementia. (PubMed id 19641318)1 FehAcr A....Janka Z. (2009)

External Searches for CHRFAM7A gene

(in PubMed, OMIM, and NCBI Bookshelf)
About This Section
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NCBI Bookshelf
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Genome Databases showing CHRFAM7A gene

(According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
About This Section
Entrez Gene: 89832 HGNC: 15781 AceView: CHRNA7 Ensembl:ENSG00000166664 euGenes: HUgn89832
ECgene: CHRFAM7A H-InvDB: CHRFAM7A

Other Databases showing CHRFAM7A gene

(According to HUGE)
About This Section
   --

Specialized Databases showing CHRFAM7A gene

(According to ATLAS, HORDE, IMGT, MTDB, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot)
About This Section
   --

Intellectual Property
for CHRFAM7A gene

(Patent information from GeneIP,
Licensable technologies from WIS Yeda, Salk, Tufts,
IP news from XenneX, Inc.)
About This Section
Patent Information for CHRFAM7A gene:
Search GeneIP for patents involving CHRFAM7A

GeneCards and IP:
Japan Patent Office Licenses GeneCards     European Patent Office Licenses GeneCards     Improving the IP Search



Products
for CHRFAM7A gene

(Antibodies, recombinant proteins, and assays by Millipore, Sigma-Aldrich, R&D Systems, Qiagen, GenScript, Cell Signaling Technology, SABiosciences, Novus Biologicals, Epitomics, ProSpec, Uscn,
Clones available from Millipore, Sigma-Aldrich, OriGene, GenScript, Sino Biological, PCR Arrays from SABiosciences, Drugs and/or compounds by Sigma-Aldrich, Tocris Bioscience, and/or Enzo Life Sciences)
About This Section

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 QIAGEN Custom miScript Target Protector blocks miRNA-binding site of CHRFAM7A
 SeqTarget long-range PCR primers for resequencing CHRFAM7A
 QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays
 QIAGEN FlexiTube/FlexiPlate siRNA for gene silencing of CHRFAM7A
 GenScript Custom Purified and Recombinant Proteins Services for CHRFAM7A GenScript cDNA clones with any tag delivered in your preferred vector for CHRFAM7A
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 Browse antibodies at Epitomics
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 ELISAs and CLIAs for CHRFAM7A
       

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