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

SNORD1C Gene

RNA gene   GIFtS: 16
GCID: GC17P074560

small nucleolar RNA, C/D box 1C
  Search for SNORD1C
in
MalaCards
our new
 Human Malady Compendium 
Biological research products
for SNORD1C    

Aliases
for SNORD1C gene

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, and/or 10fRNAdb)
About This Section
Subcategory (RNA class): snoRNA

Quality score for this RNA gene is 6

Aliases
Small Nucleolar RNA, C/D Box 1C1 2
R38C1 2
SnR38C1

External Ids:    HGNC: 326771   Entrez Gene: 6778502   Ensembl: ENSG000002001857   
ORGUL members:    fRNAdb10:FR161121 FR399504 FR295794 FR328196 FR161121      
NCBI:AJ543326 AJ543326 BC042949 AK123993 AC015802    
NONCODE:u3120    
Rfam:RF00213    
RNAdb:SNO1381    

Export aliases for SNORD1C gene to outside databases

Previous GC identifers: GC17U900726 GC17P072079 GC17P074553 GC17P069982


Summaries
for SNORD1C gene

(According to Entrez Gene, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
About This Section
fRNAdb sequence ontology for SNORD1C:
C_D_box_snoRNA - Most box C/D snoRNAs also contain long (>10 nt) sequences complementary to rRNA. Boxes C and D, as well as boxes C' and D', are usually located in close proximity, and form a structure known as the box C/D motif. This motif is important for snoRNA stability, processing, nucleolar targeting and function. A small number of box C/D snoRNAs are involved in rRNA processing; most, however, are known or predicted to serve as guide RNAs in ribose methylation of rRNA. Targeting involves direct base pairing of the snoRNA at the rRNA site to be modified and selection of a rRNA nucleotide a fixed distance from box D or D'.

View fRNAdb secondary structures for SNORD1C

Genomic Views
for SNORD1C 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 69), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section
 Regulatory elements:
   SABiosciences Regulatory transcription factor binding sites in the SNORD1C gene promoter:
         E2F-3a   E2F-4   E2F-5   GATA-3   RelA   E2F-2   NF-kappaB   E2F-1   E2F   NF-kappaB1   
         Other transcription factors

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Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat SNORD1C


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

Entrez Gene cytogenetic band: 17q25.1   Ensembl cytogenetic band:  17q25.1   HGNC cytogenetic band: 17q25.1

SNORD1C Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
SNORD1C gene location

GeneLoc information about chromosome 17         GeneLoc Exon Structure

GeneLoc location for GC17P074560:  view genomic region     (about GC identifiers)

Start:
 74,554,873 bp from pter      End:
 74,554,951 bp from pter
Size:
 79 bases      Orientation:
 plus strand
ORGUL member locations:
Legend (see complete legend)

  • FR0399504
  • FR0295794
  • FR0161121
  • FR0328196
74554871 74554911 74554951 chr17

Proteins
for SNORD1C gene

(According to 1UniProtKB, HORDE, neXtProt, Ensembl, and/or Reactome, Modification sites according to 2PhosphoSitePlus, Specific Peptides from DME, Protein expression images according to data from SPIRE MOPED and PaxDb, 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 Uscn,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Uscn, Ontologies according to Gene Ontology Consortium 01 Mar 2013 and Entrez Gene, Antibodies by EMD Millipore, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, Abcam, and/or Uscn)
About This Section
UniProtKB: --

Protein Domains /
Families
for SNORD1C gene

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

Function
for SNORD1C gene

(According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013,
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, Clones from EMD Millipore, OriGene, SwitchGear Genomics, GenScript, Sino Biological, DNA2.0, and Vector BioLabs, Cell Lines from GenScript, LifeMap BioReagents, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Mar 2013 via Entrez Gene.)
About This Section
miRNA
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Inhib. RNA
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In Situ Assay
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Pathways & Interactions
for SNORD1C gene

(Pathways according to EMD Millipore, R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, 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 Mar 2013 via Entrez Gene).
About This Section



Interactions:

    Search SABiosciences Gene Network CentralTM Interacting Genes and Proteins Networks for SNORD1C

Drugs & Compounds
for SNORD1C gene

(Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience HMDB, BitterDB, and/or Novoseek, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB, with drugs/clinical trials/news search links to CenterWatch)
About This Section
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Browse Tocris compounds for SNORD1C
Search CenterWatch for drugs/clinical trials and news about SNORD1C 

Transcripts
for SNORD1C gene

(Secondary structures according to fRNAdb,
GenBank/EMBL/DDBJ Accessions according to
Unigene (Build 235 Homo sapiens; Mar 10 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,
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, Primers from OriGene, SABiosciences, and/or QIAGEN )
About This Section
 4 fRNAdb Secondary structures:


1 Ensembl transcript including schematic representation, and UCSC links where relevant:
ENST00000363315(snoRNA)

miRNA
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Inhib. RNA
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Primer
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GeneLoc Exon Structure


Expression
for SNORD1C 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™, 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 SNORD1C:none

SNORD1C expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS
CGAP TAG: --

Microarray
RNAseq (Illumina Body Map)
(100×FPKM)½
SAGE (Serial Analysis of Gene Expression)
About this image    SABiosciences Custom PCR Arrays for SNORD1C
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In Situ
Assay Products: 
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Orthologs
for SNORD1C 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)
About This Section
This gene was present in the common ancestor of human and mouse.

Orthologs for SNORD1C gene from 1 species (see representative species )    About this table
Organism Taxonomic
classification		 Gene Description Human
Similarity		 Orthology
Type		 Details
mouse
(Mus musculus)		 Mammalia Snord1c5 small nucleolar RNA, C/D box 1C   --   11 (81.49 cM) 116672506 


ENSEMBL Gene Tree for SNORD1C (if available)
TreeFam Gene Tree for SNORD1C (if available) 

Paralogs
for SNORD1C gene

(Paralogs according to 1HomoloGene,
2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
About This Section
  --

Genomic Variants
for SNORD1C gene

(SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, UniProtKB, 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

10/38 NCBI SNPs in SNORD1C are shown (see all 38)     About this table
Genomic DataTranscription Related DataAllele Frequencies
SNP IDValidClinical
significance		Chr 17 posSequence#AA
Chg		TypeMore#Allele
freq		PopTotal
sample		More
----------
rs343165101,2
C,--74552944(+) ATAGTG/TAGACC 5 -- us2k1 int15Minor allele frequency- T:0.09NA WA EA 362
rs1826900491,2
--74552976(+) AATCAC/GCTGGG 5 -- int1 us2k10--------
rs1439810341,2
--74552983(+) TGGGCA/GTGGTG 5 -- us2k1 int10--------
rs1443613601,2
--74552996(+) GCTCGC/TCTGTC 5 -- us2k1 int10--------
rs1127066641,2
C,--74553007(+) GTCCCG/AGCCAC 5 -- us2k1 int12Minor allele frequency- A:0.20WA 120
rs1870677081,2
--74553032(+) CGGGAG/TGATCA 5 -- int1 us2k10--------
rs1907009111,2
--74553064(+) CTACAA/GTAAGT 5 -- int1 us2k10--------
rs1831611861,2
--74553086(+) CACTGC/TACTCC 5 -- int1 us2k10--------
rs1882961411,2
--74553127(+) AAAAAC/TAAACC 5 -- us2k1 int10--------
rs2020682941,2
--74553148(+) GAAAC-/AAAAAA 5 -- int1 us2k10--------

HapMap Linkage Disequilibrium report for SNORD1C (74554873 - 74554951 bp)
Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions)
      Database of Genomic Variants (DGV) variations for SNORD1C: --

SABiosciences Cancer Mutation PCR Assays
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Disorders / Diseases
for SNORD1C 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.)
About This Section
   --

Publications
for SNORD1C 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)
About This Section

PubMed articles for SNORD1C gene, integrated from 9 sources (see all 11):
(articles sorted by number of sources associating them with SNORD1C)		    Utopia: connect your pdf to the dynamic
world of online information

  1. Identification of a novel box C/D snoRNA from mouse nucleolar cDNA library. (PubMed id 14960365)1, 3 Zhou H....Qu L.H. (2004)
  2. Eukaryotic snoRNAs: a paradigm for gene expression fl exibility. (PubMed id 19446021)1 Dieci G....Montanini B. (2009)
  3. (PubMed id 8797828)10 
  4. (PubMed id 10736225)10 
  5. (PubMed id 15608158)10 
  6. (PubMed id 7667877)10 
  7. (PubMed id 11266566)10 
  8. (PubMed id 12736310)10 
  9. (PubMed id 2247610)10 
  10. (PubMed id 16381836)10 

External Searches for SNORD1C gene

(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)

Genome Databases showing SNORD1C gene

(According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
About This Section
Entrez Gene: 677850 HGNC: 32677 Ensembl:ENSG00000200185 euGenes: HUgn677850 ECgene: SNORD1C
H-InvDB: SNORD1C

Other Databases showing SNORD1C gene

(According to HUGE)
About This Section
   --

Specialized Databases showing SNORD1C gene

(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 SNORD1C Pharmacogenomics, SNPs, Pathways

Intellectual Property
for SNORD1C gene

(Patent information from GeneIP,
Licensable technologies from WIS Yeda, Salk, Tufts,
IP news from LifeMap Sciences, Inc.)
About This Section
Patent Information for SNORD1C gene:
Search GeneIP for patents involving SNORD1C

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



Products
for SNORD1C gene

(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, Uscn, Thermo Fisher Scientific, Gene Editing from DNA2.0, Clones from EMD Millipore, OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, 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),
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