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

SNHG12 Gene

RNA gene   GIFtS: 30
GCID: GC01M028905

Small Nucleolar RNA Host Gene 12 (Non-Protein Coding)

(Previous name: chromosome 1 open reading frame 79)
(Previous symbol: C1orf79)
  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

Subcategory (RNA class): lncRNA

Quality score for this RNA gene is 3

Aliases
Small Nucleolar RNA Host Gene 12 (Non-Protein Coding)1 2     NCRNA001002
C1orf791 2 3     RP4-669K10.52
Chromosome 1 Open Reading Frame 791     TRG-113
Long Intergenic Non-Protein Coding RNA 1001     Transformation-Related Gene 11 Protein3
LINC001002     

External Ids:    HGNC: 300621   Entrez Gene: 850282   Ensembl: ENSG000001979897   UniProtKB: Q9BXW33   
ORGUL members:         
NONCODE14:n379255 n379180 n379183 n379217 n379215 see all 13      

Export aliases for SNHG12 gene to outside databases

Previous GC identifers: GC01U902257 GC01M028784


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

GeneCards Summary for SNHG12 Gene: 
SNHG12 (small nucleolar RNA host gene 12 (non-protein coding)) is an RNA gene, and is affiliated with the lncRNA class. Diseases associated with SNHG12 include mast cell neoplasm, and filariasis.


(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_000001.10  NC_018912.2  NT_004610.19  
Regulatory elements:
   SABiosciences Regulatory transcription factor binding sites in the SNHG12 gene promoter:
         GR   AML1a   GR-beta   Meis-1b   AREB6   SEF-1 (1)   Meis-1a   GR-alpha   TGIF   Meis-1   
         Other transcription factors

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Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat SNHG12


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

Entrez Gene cytogenetic band: 1p35.3   Ensembl cytogenetic band:  1p35.3   HGNC cytogenetic band: 1p35.3

SNHG12 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
SNHG12 gene location

GeneLoc information about chromosome 1         GeneLoc Exon Structure

GeneLoc location for GC01M028905:  view genomic region     (about GC identifiers)

Start:
28,905,050 bp from pter      End:
28,909,495 bp from pter
Size:
4,446 bases      Orientation:
minus strand
ORGUL member locations:
Legend (see complete legend)

ORGUL Member Locations for SNHG12

(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: SNH12_HUMAN, Q9BXW3 (See protein sequence)
Recommended Name: Putative uncharacterized protein SNHG12  
Size: 62 amino acids; 6988 Da
Caution: Product of a dubious CDS prediction

Explore the universe of human proteins at neXtProt for SNHG12: NX_Q9BXW3

SNHG12 Protein expression data from MOPED1, PaxDb2 and MAXQB3 : --

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(According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
About This Section
HGNC Gene Families: 
LNCRNA: Long non-coding RNAs

ProtoNet protein and cluster: Q9BXW3


(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

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 SNHG12

(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 SNHG12 (SNH12)

Search CenterWatch for drugs/clinical trials and news about SNHG12

(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,
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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 SNHG12 gene: 
NM_053040.1  

Unigene Cluster for SNHG12:

Small nucleolar RNA host gene 12 (non-protein coding)
Hs.632377  [show with all ESTs]
Unigene Representative Sequence: BC111553
15 Ensembl transcripts including schematic representations, and UCSC links where relevant:
ENST00000464612 ENST00000475441 ENST00000531126 ENST00000461448(uc001bqn.3)
ENST00000470977(uc001bqk.3 uc001bql.3) ENST00000474814(uc001bqo.3)
ENST00000481368(uc001bqm.3) ENST00000481220 ENST00000488745 ENST00000483436
ENST00000464115 ENST00000461832 ENST00000384581(uc001bqr.2) ENST00000384584(uc001bqs.2)
ENST00000384342(uc001bqt.2)
miRNA
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Additional mRNA sequence: 

AF277181.1 AJ609433.1 AJ609451.1 AJ609466.1 AK092096.1 AY277594.1 BC022205.1 BC034611.1 
BC045792.1 BC064589.1 BC068048.1 BC107730.1 BC111553.1 NR_002976.1 NR_002987.1 NR_003035.1 
NR_024127.1 

11 DOTS entries:

DT.100026537  DT.40277411  DT.99996968  DT.87015908  DT.100817708  DT.211434  DT.432523  DT.100026540 
DT.95294171  DT.100817710  DT.97841807 

24/91 AceView cDNA sequences (see all 91):

BM142620 BU732252 AI962298 BC045792 BU689408 AA581708 CB178688 AA902170 
AA905228 AA417948 AK092096 CB178449 BM785231 BU786162 BE794361 BM796569 
AI867793 BC064589 AA631621 AI401149 BM762937 AI740812 BU633154 BC068048 

GeneLoc Exon Structure

5/10 Alternative Splicing Database (ASD) splice patterns (SP) for SNHG12 (see all 10)    About this scheme

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


ECgene alternative splicing isoforms for SNHG12

(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

Expression evidence for SNHG12:none

SNHG12 expression in normal human tissues (normalized intensities)      SNHG12 embryonic expression: see
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS <intensity>2/3
CGAP TAG: CTAATGCAAA
SNHG12 Expression
About this image


SNHG12 expression in embryonic tissues and stem cells    About this table
Data from LifeMap, the Embryonic Development and Stem Cells Database 
 5/5 selected tissues (see all 5) fully expand
 
 Endothelium (Cardiovascular System)    fully expand to see all 2 entries
         Umbilical cord blood-derived endothelial progenitor cells
         cd31+ cells   
 
 Blood (Cardiovascular System)    fully expand to see all 2 entries
         monocyte-derived macrophage   
 
 Umbilical Cord (Extraembryonic Tissues)
         Umbilical cord blood-derived endothelial progenitor cells
 
 Eye (Sensory Organs)
         lens   
 
 Cartilage (Muscoskeletal System)
         fetal cartilage   

Genevestigator expression for SNHG12

SOURCE GeneReport for Unigene cluster: Hs.632377
    SABiosciences Custom PCR Arrays for SNHG12
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In Situ
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(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 human and mouse.

Orthologs for SNHG12 gene from 1 species (see representative species )    About this table
Organism Taxonomic
classification
Gene Description Human
Similarity
Orthology
Type
Details
mouse
(Mus musculus)
Mammalia Snhg125 small nucleolar RNA host gene 12   --   4 (65.16 cM) 132308678 


ENSEMBL Gene Tree for SNHG12 (if available)
TreeFam Gene Tree for SNHG12 (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

10/16 SNPs in SNHG12 are shown (see all 16)    About this table     
Genomic DataTranscription Related DataAllele Frequencies
SNP IDValidClinical
significance
Chr 1 posSequence#AA
Chg
TypeMore#Allele
freq
PopTotal
sample
More
----------
rs1892500901,2
--28909681(+) ACATCA/TCATGT 1 -- us2k10--------
rs1807952901,2
--28909738(+) ATAATA/CTGACT 1 -- us2k10--------
rs1864924561,2
--28909830(+) TTGCTC/TCCGAC 1 -- us2k10--------
rs1902051011,2
--28909991(+) ATCTCA/GGCTCA 1 -- us2k10--------
rs617860211,2
C--28910008(+) GCTCCC/GGCTCC 1 -- us2k10--------
rs617860221,2
C--28910009(+) CTCCCC/GCTCCC 1 -- us2k10--------
rs1817487871,2
--28910022(+) GTTCAC/TGCCAT 1 -- us2k10--------
rs1861303701,2
--28910233(+) TACGCA/TTTAAA 1 -- us2k10--------
rs1117524591,2
----28909947(+) GAGACA/GGAGCT 1 -- us2k11Minor allele frequency- G:0.00CSA 1
rs1134862101,2
----28910164(+) GATCCA/TCCCGC 1 -- us2k10--------

HapMap Linkage Disequilibrium report for SNHG12 (28905050 - 28909495 bp)

Structural Variations
     Database of Genomic Variants (DGV) 1 variation for SNHG12:    About this table     
Variant IDTypeSubtypePubMed ID
esv2671121CNV Deletion23128226

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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
2 diseases for SNHG12:    About MalaCards
mast cell neoplasm    filariasis

1 disease from the University of Copenhagen DISEASES database for SNHG12:
Mast cell neoplasm

SNHG12 for disorders           About GeneDecksing


Export disorders for SNHG12 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 SNHG12 gene integrated from 9 sources:
(articles sorted by number of sources associating them with SNHG12)
    Utopia: connect your pdf to the dynamic
world of online information

  1. The DNA sequence and biological annotation of human chromosome 1. (PubMed id 16710414)1, 2 Gregory S.G.... Bentley D.R. (2006)
  2. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1 Ota T.... Sugano S. (2004)
  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. (2002)
  4. Hepatitis C virus core protein interacts with 14-3-3 protein and activates the kinase Raf-1. (PubMed id )2 Aoki H.... Hino O. (2000)

(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: 85028 HGNC: 30062 AceView: LOC85028 Ensembl:ENSG00000197989 euGenes: HUgn85028
ECgene: SNHG12 H-InvDB: SNHG12

(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 SNHG12 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 SNHG12 gene:
Search GeneIP for patents involving SNHG12

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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 inGenious Targeting Laboratory - Custom generated mouse model solutions for SNHG12
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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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