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Category   Symbol Source: HGNC EntrezGene Ensembl GeneCards RNA genes CroW21
GIFtS

C12orf39 Gene

protein-coding   GIFtS: 40
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)
About This Section

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   

Export aliases for C12orf39 gene to outside databases

Previous GC identifers: GC12P021574 GC12P021453


(According to Entrez Gene, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
About This Section

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

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 73), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section
RefSeq DNA sequence:
NC_000012.11  NC_018923.2  NT_009714.17  
Regulatory elements:
   SABiosciences 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 SABiosciences Chromatin IP Primers for C12orf39

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays 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 UniProtKB, HORDE, neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MAXQB 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., Ontologies according to Gene Ontology Consortium 01 Oct 2013 and Entrez Gene, Antibodies by EMD Millipore, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, and/or Cloud-Clone Corp.)
About This Section

UniProtKB/Swiss-Prot: SPXN_HUMAN, Q9BT56 (See protein sequence)
Recommended Name: Spexin precursor  
Size: 116 amino acids; 13302 Da
Subcellular location: Secreted. Cytoplasmic vesicle, secretory vesicle
Secondary accessions: B3KND6

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

Explore proteomics data for C12orf39 at MOPED 

C12orf39 Protein expression data from MOPED1, PaxDb2 and MAXQB3 :    About this image 

C12orf39 Protein Expression

REFSEQ proteins: NP_085049.1  
ENSEMBL proteins: 
 ENSP00000256969   ENSP00000440877  

Human Recombinant Protein Products for C12orf39: 
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Cloud-Clone Corp. Proteins for C12orf39 

Gene Ontology (GO): 5 cellular component terms (GO ID links to tree view):    About this table

GO IDQualified GO termEvidencePubMed IDs
GO:0005576extracellular region IEA--
GO:0005634nucleus IDA--
GO:0005730NOT nucleolus IDA--
GO:0030133transport vesicle IEA--
GO:0043231intracellular membrane-bounded organelle IDA--

C12orf39 for ontologies           About GeneDecksing



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(According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
About This Section

ProtoNet protein and cluster: Q9BT56


(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,
bound targets from SABiosciences, miRNA Gene Targets from miRTarBase, shRNA from OriGene, RNAi from EMD Millipore, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, Gene Editing from DNA2.0, Sirion Biotech, Clones from EMD Millipore, OriGene, SwitchGear Genomics, GenScript, Sino Biological, DNA2.0, Vector BioLabs, and Sirion Biotech, Cell Lines from GenScript, LifeMap BioReagents, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Oct 2013 via Entrez Gene.)
About This Section

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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(Pathways according to EMD Millipore, 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 SABiosciences, 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 Oct 2013 via Entrez Gene).
About This Section



Interactions:

    Search SABiosciences Gene Network CentralTM Interacting Genes and Proteins Networks for C12orf39

(Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB, with drugs/clinical trials/news search links to CenterWatch)
About This Section
Browse Small Molecules at EMD Millipore
Browse drugs & compounds from Enzo Life Sciences

Browse Tocris compounds for C12orf39 (SPXN)

Search CenterWatch for drugs/clinical trials and news about 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,
Conferences by KenesGroup, exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
RNAi Products from EMD Millipore,
siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN,
Tagged/untagged cDNA clones from OriGene, SwitchGear Genomics, GenScript, DNA2.0, Vector BioLabs, Sirion Biotech, Primers from OriGene, SABiosciences, and/or QIAGEN )
About This Section

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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  QIAGEN 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 

24/60 AceView cDNA sequences (see all 60):

AI357886 AI590178 AI628995 AI985275 BQ216128 AW242599 AI796722 AA774561 
BX492053 BI756561 AI928358 CA429960 AI003498 AW300393 BG332802 AI671735 
AI768038 AI948777 AA569948 BX433469 BM807909 BC004336 BF197316 AW015733 

GeneLoc Exon Structure

5/6 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™, plus additional links to Genevestigator, and/or SOURCE, and/or BioGPS, and/or UniProtKB,
PCR Arrays from SABiosciences, Primers from OriGene, SABiosciences, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
About This Section

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


C12orf39 expression in embryonic tissues and stem cells    About this table
Data from LifeMap, the Embryonic Development and Stem Cells Database 
 5/4 selected tissues (see all 4) fully expand
 
 Pancreas (Endocrine System)
         Pancreatic endoderm/endocrine precursor-like cells ( A scalable, suspension protocol...
 
 Endothelium (Cardiovascular System)
         Human corneal endothelial cells
 
 Eye (Sensory Organs)
         Human corneal endothelial cells
 
 Kidney (Urinary System)

See C12orf39 Protein Expression from SPIRE MOPED and PaxDB
Genevestigator expression for C12orf39

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

    SABiosciences Custom PCR Arrays for C12orf39
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QIAGEN QuantiFast Probe-based Assays in human, mouse, rat C12orf39
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)
About This Section

This gene was present in the common ancestor of chordates.

Orthologs for C12orf39 gene from 4/9 species (see all 9)    About this table
Organism Taxonomic
classification
Gene Description Human
Similarity
Orthology
Type
Details
chicken
(Gallus gallus)
Aves C12ORF396
Uncharacterized protein
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 C4H12orf396
chromosome 12 open reading frame 39
50(a)
1 ↔ 1
4(15862602-15868415)
        Species with no ortholog for C12orf39

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)
About This Section
  --

(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) and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers from QIAGEN, Cancer Mutation PCR Arrays and Assays and Copy Number PCR Arrays from SABiosciences)
About This Section

10/160 SNPs in C12orf39 are shown (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

SABiosciences Cancer Mutation PCR Assays
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(in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Conferences by KenesGroup, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
About This Section
5 diseases for C12orf39:    About MalaCards
discitis    locked-in syndrome    agoraphobia    radiculopathy
spondylosis

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)
About This Section

PubMed articles for C12orf39 gene integrated from 9 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. (2012)
  2. Evolutionary sequence modeling for discovery of peptide hormones. (PubMed id 19132080)1, 2 Sonmez K.... Toll L. (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. (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. (2004)
  5. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1, 2 Ota T.... Sugano S. (2004)
  6. 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. (2002)
  7. Interactions of pathological hallmark proteins: tubul in polymerization promoting protein/p25, beta-amyloid, and alpha-synuclein. (PubMed id 21832049)1 OlA!h J....OvA!di J. (2011)
  8. C12ORF39, a novel secreted protein with a typical amidation processing signal. (PubMed id 19193193)1 Wan B....Han Z.G. (2009)
  9. Toward a confocal subcellular atlas of the human proteome. (PubMed id 18029348)1 Barbe L....Andersson-Svahn H. (2008)
  10. 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. (2005)

(in PubMed, OMIM, and NCBI Bookshelf)
About This Section
 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)
About This Section
Entrez Gene: 80763 HGNC: 28139 AceView: MGC10946 Ensembl:ENSG00000134548 euGenes: HUgn80763
ECgene: C12orf39 H-InvDB: C12orf39

(According to HUGE)
About This Section
  --

(According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot)
About This Section
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.)
About This Section
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, SABiosciences, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Cloud-Clone Corp., Thermo Fisher Scientific, LSBio, Gene Editing from DNA2.0 and Sirion Biotech, Clones from EMD Millipore, OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Sirion Biotech, Cell lines from GenScript, and LifeMap BioReagents, PCR Arrays from SABiosciences, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, and/or Enzo Life Sciences, In Situ Hybridization Assays from
Advanced Cell Diagnostics, Animal models from inGenious Targeting Laboratory, genOway)
About This Section

 
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GeneCards Homepage - Last full update: 23 Oct 2013 - Incrementals: 4 Nov 2013 , 7 Nov 2013 , 23 Jan 2014

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transforming growth factor, beta 1
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