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C12orf39 Gene

protein-coding   GIFtS: 42
GCID: GC12P021679

Chromosome 12 Open Reading Frame 39

  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)
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This gene clusters with an RNA gene
Subcategory (RNA class): antisense

Quality score for the ORGUL clustered with this gene is 3

Aliases
Chromosome 12 Open Reading Frame 391 2
Neuropeptide Q1 2
NPQ2 3
spexin2

External Ids:    HGNC: 281391   Entrez Gene: 807632   Ensembl: ENSG000001345487   UniProtKB: Q9BT563   
ORGUL members:         

Export aliases for C12orf39 gene to outside databases

Previous GC identifers: GC12P021574 GC12P021453


(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 C12orf39 Gene:
C12orf39 (chromosome 12 open reading frame 39) is a protein-coding gene. Diseases associated with C12orf39 include locked-in syndrome, and discitis.

UniProtKB/Swiss-Prot: SPXN_HUMAN, Q9BT56
Function: Induces contraction of stomach muscle




(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_000012.12  NC_018923.2  NT_009714.18  
Regulatory elements:
   Regulatory transcription factor binding sites in the C12orf39 gene promoter:
         STAT5B   TBP   Sox5   CUTL1   POU3F2   C/EBPalpha   IRF-2   HFH-1   TGIF   NF-AT1   
         Other transcription factors

Browse SwitchGear Promoter luciferase reporter plasmids
   Search Chromatin IP Primers for C12orf39

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat C12orf39


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

Entrez Gene cytogenetic band: 12p12.1   Ensembl cytogenetic band:  12p12.1   HGNC cytogenetic band: 12p12.1

C12orf39 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
C12orf39 gene location

GeneLoc information about chromosome 12         GeneLoc Exon Structure

GeneLoc location for GC12P021679:  view genomic region     (about GC identifiers)

Start:
21,679,241 bp from pter      End:
21,690,311 bp from pter
Size:
11,071 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: SPXN_HUMAN, Q9BT56 (See protein sequence)
Recommended Name: Spexin precursor  
Size: 116 amino acids; 13302 Da
Secondary accessions: B3KND6

Explore the universe of human proteins at neXtProt for C12orf39: NX_Q9BT56

Explore proteomics data for C12orf39 at MOPED


See C12orf39 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

REFSEQ proteins: NP_085049.1  
ENSEMBL proteins: 
 ENSP00000256969   ENSP00000440877  

C12orf39 Human Recombinant Protein Products:

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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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1 InterPro protein domain:
 IPR028126 Spexin

Graphical View of Domain Structure for InterPro Entry Q9BT56

ProtoNet protein and cluster: Q9BT56


C12orf39 for domains           About GeneDecksing


(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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Molecular Function:

     UniProtKB/Swiss-Prot Summary: SPXN_HUMAN, Q9BT56
Function: Induces contraction of stomach muscle

Phenotypes:
     2 GenomeRNAi human phenotypes for C12orf39:

 Increased cell number in G2M,   Wnt reporter downregulated 

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 UniProtKB/Swiss-Prot
SPXN_HUMAN, Q9BT56: Secreted. Cytoplasmic vesicle, secretory vesicle
Subcellular locations from COMPARTMENTS: 

CompartmentConfidence
extracellular5
nucleus4
chloroplast3

Gene Ontology (GO): 4 cellular component terms:    About this table

GO IDQualified GO termEvidencePubMed IDs
GO:0005576extracellular region IEA--
GO:0005634nucleus ----
GO:0030133transport vesicle IEA--
GO:0043231intracellular membrane-bounded organelle ----

C12orf39 for ontologies           About GeneDecksing


(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 C12orf39
Interactions:

    Search GeneGlobe Interaction Network for C12orf39

(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 C12orf39 (SPXN)



(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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REFSEQ mRNAs for C12orf39 gene: 
NM_030572.2  

Unigene Cluster for C12orf39:

Chromosome 12 open reading frame 39
Hs.130692  [show with all ESTs]
Unigene Representative Sequence: AK075342
7 Ensembl transcripts including schematic representations, and UCSC links where relevant:
ENST00000256969(uc001rfa.1) ENST00000535033 ENST00000546199 ENST00000544637
ENST00000535139(uc009ziv.1) ENST00000543800(uc009ziw.1) ENST00000537527

miRNA
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  QuantiFast Probe-based Assays in human, mouse, rat C12orf39

Additional mRNA sequence: 

AK027273.1 AK075342.1 AK311147.1 AK311217.1 BC004336.1 

7 DOTS entries:

DT.405326  DT.65287648  DT.121121776  DT.121121715  DT.121121779  DT.95157475  DT.91864363 

Selected AceView cDNA sequences (see all 60):

AI985275 AI590178 AA774561 BQ216128 AI357886 AI796722 AW242599 AI628995 
AK027273 BM807909 AW195026 AI671735 BG332802 AI768038 BE326710 BI765315 
BU618991 BE466344 BF197316 BQ773197 AW300393 AI948777 BX508540 AA569948 

GeneLoc Exon Structure

Selected Alternative Splicing Database (ASD) splice patterns (SP) for C12orf39 (see all 6)    About this scheme

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


ECgene alternative splicing isoforms for C12orf39

(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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C12orf39 expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS <intensity>2/3
CGAP TAG: TTAATTATTT
C12orf39 Expression
About this image

C12orf39 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

C12orf39 Protein Expression

SOURCE GeneReport for Unigene cluster: Hs.130692

UniProtKB/Swiss-Prot: SPXN_HUMAN, Q9BT56
Tissue specificity: Expressed in submucosal layer of esophagus and stomach fundus. Expressed in brain, pancreas
and kidney

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In Situ
Assay Products:
 

 
Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for C12orf39

(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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This gene was present in the common ancestor of chordates.

Orthologs for C12orf39 gene from Selected species (see all 9)    About this table
Organism Taxonomic
classification
Gene Description Human
Similarity
Orthology
Type
Details
mouse
(Mus musculus)
Mammalia B230216G23Rik1 RIKEN cDNA B230216G23 gene 76.15(n)
67.24(a)
  319552  NM_001242345.1  NP_001229274.1 
chicken
(Gallus gallus)
Aves C12orf396
chromosome 12 open reading frame 39
57(a)
1 ↔ 1
1(67263650-67266854)
lizard
(Anolis carolinensis)
Reptilia C12orf396
chromosome 12 open reading frame 39
49(a)
1 ↔ 1
5(6291944-6303886)
African clawed frog
(Xenopus laevis)
Amphibia BU901521.12   -- 78.05(n)    BU901521.1 
zebrafish
(Danio rerio)
Actinopterygii LOC1018825351 spexin-like 55(n)
51(a)
  101882535  XM_005164774.1  XP_005164831.1 


ENSEMBL Gene Tree for C12orf39 (if available)
TreeFam Gene Tree for C12orf39 (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 C12orf39 (see all 160)    About this table    
Genomic DataTranscription Related DataAllele Frequencies
SNP IDValidClinical
significance
Chr 12 posSequence#AA
Chg
TypeMore#Allele
freq
PopTotal
sample
More
----------
rs341917251,2
C,F--21677311(+) ATTCAA/GCCAAC 1 -- us2k14Minor allele frequency- G:0.04NA 126
rs1421865951,2
--21677347(+) CCATCA/GTATTC 1 -- us2k10--------
rs108418411,2
C,F,A,H--21677454(+) TTCTCC/TTTTCT 1 -- us2k1 trp320Minor allele frequency- T:0.32NS EA NA WA 2348
rs1924288161,2
--21677500(+) CCTCTG/TCTCAT 1 -- us2k10--------
rs1444775501,2
--21677541(+) CCTGCA/CACTCT 1 -- us2k10--------
rs1456299181,2
--21677771(+) ATTTTA/GATATG 1 -- us2k10--------
rs730813071,2
C--21677865(+) CCCACA/CGTTTT 1 -- us2k13Minor allele frequency- C:0.14CSA WA NA 240
rs123027871,2
H--21677885(+) cctaaG/Aaatca 1 -- us2k14Minor allele frequency- A:0.00NS EA 414
rs768186171,2
F--21677974(+) CCAAAT/GTCATT 1 -- us2k11Minor allele frequency- G:0.04NA 120
rs571150571,2
F--21677996(+) TTTCCC/TTGTGT 1 -- us2k11Minor allele frequency- T:0.01EA 120

HapMap Linkage Disequilibrium report for C12orf39 (21679241 - 21690311 bp)

Structural Variations
     Database of Genomic Variants (DGV) 3 variations for C12orf39:    About this table    
Variant IDTypeSubtypePubMed ID
nsv898897CNV Loss21882294
nsv528556CNV Gain19592680
nsv898896CNV Gain21882294

Site Specific Mutation Identification with PCR Assays
Search QIAGEN SeqTarget long-range PCR primers for resequencing C12orf39
DNA2.0 Custom Variant and Variant Library Synthesis for C12orf39

(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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6 diseases for C12orf39:    
About MalaCards
locked-in syndrome    discitis    agoraphobia    radiculopathy
spondylosis    endotheliitis

3 diseases from the University of Copenhagen DISEASES database for C12orf39:
locked-in syndrome     Agoraphobia     Spondylosis

C12orf39 for disorders           About GeneDecksing


Export disorders for C12orf39 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 C12orf39 gene integrated from 10 sources:
(articles sorted by number of sources associating them with C12orf39)
    Utopia: connect your pdf to the dynamic
world of online information

  1. Peptides derived from the prohormone proNPQ/spexin are potent central modulators of cardiovascular and renal function and nociception. (PubMed id 22038051)1, 3 Toll L....Kapusta D.R. (FASEB J. 2012)
  2. Evolutionary sequence modeling for discovery of peptide hormones. (PubMed id 19132080)1, 2 Sonmez K.... Toll L. (PLoS Comput. Biol. 2009)
  3. Identification of novel peptide hormones in the human proteome by hidden Markov model screening. (PubMed id 17284679)1, 2 Mirabeau O.... Gross C. (Genome Res. 2007)
  4. 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)
  5. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1, 2 Ota T.... Sugano S. (Nat. Genet. 2004)
  6. Interactions of pathological hallmark proteins: tubulin polymerization promoting protein/p25, beta-amyloid, and alpha-synuclein. (PubMed id 21832049)1 OlA!h J....OvA!di J. (J. Biol. Chem. 2011)
  7. C12ORF39, a novel secreted protein with a typical amidation processing signal. (PubMed id 19193193)1 Wan B....Han Z.G. (Biosci. Rep. 2010)
  8. Toward a confocal subcellular atlas of the human proteome. (PubMed id 18029348)1 Barbe L....Andersson-Svahn H. (amp 2008)
  9. Signal sequence and keyword trap in silico for selection of full- length human cDNAs encoding secretion or membrane proteins from oligo- capped cDNA libraries. (PubMed id 16303743)1 Otsuki T....Isogai T. (DNA Res. 2005)
  10. 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: 80763 HGNC: 28139 AceView: MGC10946 Ensembl:ENSG00000134548 euGenes: HUgn80763
ECgene: C12orf39 H-InvDB: C12orf39

(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 C12orf39 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 C12orf39 gene:
Search GeneIP for patents involving C12orf39

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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GeneCards Homepage - Last full update: 7 May 2014 - Incrementals: 9 May 2014 , 2 Jun 2014 , 26 Jun 2014 , 30 Jun 2014

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