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SNORD89 Gene

RNA gene   GIFtS: 23
GCID: GC02M101889

Small Nucleolar RNA, C/D Box 89

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Aliases
for SNORD89 gene

(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): snoRNA

Quality score for this RNA gene is 3

Aliases
Small Nucleolar RNA, C/D Box 891 2
HBII-2892

External Ids:    HGNC: 327501   Entrez Gene: 6922052   Ensembl: ENSG000002122837   
ORGUL members:    fRNAdb10:FR008007      

Export aliases for SNORD89 gene to outside databases

Previous GC identifers: GC02U900834 GC02M101255 GC02M095653


Summaries
for SNORD89 gene

(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 SNORD89 Gene:
SNORD89 (small nucleolar RNA, C/D box 89) is an RNA gene, and is affiliated with the snoRNA class.


Genomic Views
for SNORD89 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 75), Regulatory elements and Epigenetics data according to QIAGEN, and/or SwitchGear Genomics)
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RefSeq DNA sequence at NCBI GenBank:
NC_000002.11  NC_018913.2  NT_005403.18  
Regulatory elements:
   Regulatory transcription factor binding sites in the SNORD89 gene promoter:
         HFH-3   RP58   USF1   AML1a   RREB-1   HNF-3beta   FOXI1   POU2F1   USF-1   POU2F1a   
         Other transcription factors

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Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat SNORD89


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

Entrez Gene cytogenetic band: 2q11.2   Ensembl cytogenetic band:  2q11.2   HGNC cytogenetic band: 2q11.2

SNORD89 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
SNORD89 gene location

GeneLoc information about chromosome 2         GeneLoc Exon Structure

GeneLoc location for GC02M101889:  view genomic region     (about GC identifiers)

Start:
 101,889,398 bp from pter      End:
 101,889,511 bp from pter
Size:
 114 bases      Orientation:
 minus strand

Proteins
for SNORD89 gene

(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., eBioscience, and/or antibodies-online,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, Cloud-Clone Corp., eBioscience, and/or antibodies-online, Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, Abcam, Cloud-Clone Corp, antibodies-online, and/or others.)
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UniProtKB: --

Domains /
Families
for SNORD89 gene

(According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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SNORD: ncRNAs / Small nucleolar RNAs : C/D box containing

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Function
for SNORD89 gene

(According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, 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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miRNA
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Localization
for SNORD89 gene

(According to UniProtKB, COMPARTMENTS Subcellular localization database, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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Pathways & Interactions
for SNORD89 gene

(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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Drugs & Compounds
for SNORD89 gene

(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 Tocris compounds for SNORD89



Transcripts
for SNORD89 gene

(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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Unigene Cluster for SNORD89:

Small nucleolar RNA, C/D box 89
Hs.656503  [show with all ESTs]
Unigene Representative Sequence: AK126261
1 Ensembl transcript including schematic representation, and UCSC links where relevant:
ENST00000390981(snoRNA)
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Additional mRNA sequence: 

AK126261.1 NR_003070.1 

3 DOTS entries:

DT.107508  DT.308472  DT.408425 

GeneLoc Exon Structure


Expression
for SNORD89 gene

(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 SNORD89:none

SNORD89 expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS <intensity>2/3
CGAP TAG: CCACACCCTG
SNORD89 Expression
About this image


SNORD89 expression in embryonic tissues and stem cells    About this table
Data from LifeMap, the Embryonic Development and Stem Cells Database
 selected tissues (see all 2) fully expand
 
 Neurons
         nGnG Amacrine Cells Inner Nuclear Layer
 
 Eye (Sensory Organs)
         nGnG Amacrine Cells Inner Nuclear Layer
SNORD89 Protein expression data from MOPED1, PaxDb2 and MaxQB3:  --

SOURCE GeneReport for Unigene cluster: Hs.656503
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Orthologs
for SNORD89 gene

(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 SNORD89 gene from Selected species (see all 9)    About this table
Organism Taxonomic
classification		 Gene Description Human
Similarity		 Orthology
Type		 Details
mouse
(Mus musculus)		 Mammalia Snord895 small nucleolar RNA, C/D box 89   --   1 (18.32 cM) 39548747 
chicken
(Gallus gallus)		 Aves SNORD896
 Small nucleolar RNA SNORD89
 82(a)
 1 ↔ 1
 1(132818250-132818363) ENSGALG00000025284
lizard
(Anolis carolinensis)		 Reptilia SNORD896
 Small nucleolar RNA SNORD89
 73(a)
 1 ↔ 1
 GL343542.1(134601-134710) ENSACAG00000020451
zebrafish
(Danio rerio)		 Actinopterygii SNORD896
 Small nucleolar RNA SNORD89
 61(a)
 1 ↔ 1
 2(32226018-32226140) ENSDARG00000083906


ENSEMBL Gene Tree for SNORD89 (if available)
TreeFam Gene Tree for SNORD89 (if available)

Paralogs
for SNORD89 gene

(Paralogs according to 1HomoloGene,
2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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Genomic Variants
for SNORD89 gene

(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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2 SNPs for SNORD89    About this table                                 

Genomic DataTranscription Related DataAllele Frequencies
SNP IDValidClinical
significance		Chr 2 posSequence#AA
Chg		TypeMore#Allele
freq		PopTotal
sample		More
----------
rs709430701,2
C--101890510(-) AAAAA-/A/AA  
        TACTG 		1 -- us2k12NA CSA 4
rs3677717241,2
----101891253(+) TTTTT-/TCTTTT 1 -- us2k10--------

HapMap Linkage Disequilibrium report for SNORD89 (101889398 - 101889511 bp)

Structural Variations
     Database of Genomic Variants (DGV) 1 variation for SNORD89:    About this table    
Variant IDTypeSubtypePubMed ID
esv34123CNV Loss18971310

Site Specific Mutation Identification with PCR Assays
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Disorders / Diseases
for SNORD89 gene

(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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Publications
for SNORD89 gene

(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 SNORD89 gene integrated from 10 sources:
(articles sorted by number of sources associating them with SNORD89)		    Utopia: connect your pdf to the dynamic
world of online information

  1. RNomics: an experimental approach that identifies 201 candidates for novel, small, non-messenger RNAs in mouse. (PubMed id 11387227)1, 3 HA1ttenhofer A....Brosius J. (EMBO J. 2001)
  2. Eukaryotic snoRNAs: a paradigm for gene expression flexibility. (PubMed id 19446021)1 Dieci G....Montanini B. (Genomics 2009)

External Searches for SNORD89 gene

(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)

Genome Databases showing SNORD89 gene

(According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
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Entrez Gene: 692205 HGNC: 32750 Ensembl:ENSG00000212283 euGenes: HUgn692205 ECgene: SNORD89
H-InvDB: SNORD89

Other Databases showing SNORD89 gene

(According to HUGE)
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Specialized Databases showing SNORD89 gene

(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 SNORD89 Pharmacogenomics, SNPs, Pathways

Intellectual Property
for SNORD89 gene

(Patent information from GeneIP,
Licensable technologies from WIS Yeda, Salk, Tufts,
IP news from LifeMap Sciences, Inc.)
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TryGeneCards Plus		Patent Information for SNORD89 gene:
Search GeneIP for patents involving SNORD89

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



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