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RNU1-2 Gene

RNA gene GIFtS: 17
GCID: GC01P017233

RNA, U1 Small Nuclear 2

(Previous names: RNA, U1C1 small nuclear, RNA, U1C2 small nuclear)
(Previous symbols: RNU1C1, RNU1C2)

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at

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(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): snRNA

Quality score for this RNA gene is 5

Aliases
RNA, U1 Small Nuclear 2¹ ²		RNA, U1C2 Small Nuclear¹
RNU1C1¹ ²		U1C1²
RNU1C2¹ ²		U1C21²
RNA, U1C1 Small Nuclear¹

External Ids:	HGNC: 10123¹	Entrez Gene: 26870²	Ensembl: ENSG00000207005⁷

ORGUL members:	fRNAdb¹⁰:FR065763 FR251069 FR135896 FR067322 FR005262
	NCBI¹³:K00788 M28011 M14586 M14385 M14386 M14587 M14585 AK026936 AC006359 V00590 M25190	see top 5
	NONCODE¹⁴:u3829 u4044
	Rfam:RF00003

Export aliases for RNU1-2 gene to outside databases

Previous GC identifers: GC01U902390 GC01P017224 GC01P017227

(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 RNU1-2 Gene:

RNU1-2 (RNA, U1 small nuclear 2) is an RNA gene, and is affiliated with the snRNA class.

fRNAdb sequence ontologies for RNU1-2 - the ORGUL cluster for this gene includes several descriptions:
snRNA - A small nuclear RNA molecule involved in pre-mRNA splicing and processing.
U1_snRNA - U1 is a small nuclear RNA (snRNA) component of the spliceosome (involved in pre-mRNA splicing). Its 5' end forms complementary base pairs with the 5' splice junction, thus defining the 5' donor site of an intron. There are significant differences in sequence and secondary structure between metazoan and yeast U1 snRNAs, the latter being much longer (568 nucleotides as compared to 164 nucleotides in human). Nevertheless, secondary structure predictions suggest that all U1 snRNAs share a 'common core' consisting of helices I, II, the proximal region of III, and IV.

View fRNAdb secondary structures for RNU1-2

(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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Regulatory elements:

Search for regulatory transcription factor binding sites for RNU1-2
Other transcription factors

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Epigenetics:

DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat RNU1-2

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

Entrez Gene cytogenetic band: 1p36.1 Ensembl cytogenetic band: 1p36.13 HGNC cytogenetic band: 1p36.13

RNU1-2 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
RNU1-2 gene location

GeneLoc information about chromosome 1 GeneLoc Exon Structure

GeneLoc location for GC01P017233: view genomic region (about GC identifiers)

Start:	17,222,475 bp from pter	End:	17,222,638 bp from pter
Size:	164 bases	Orientation:	plus strand

ORGUL member locations:
Legend (see complete legend)

ORGUL Member Locations for RNU1-2

(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.,
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UniProtKB: --

(According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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HGNC Gene Families:

snRNA: ncRNAs / Small nuclear RNAs

(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,
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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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(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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SuperPaths for RNU1-2 About

See pathways by source

SuperPath

Contained pathways About

Spliceosomal Splicing Cycle

Spliceosomal Splicing Cycle

1 Downloadable PowerPoint Slide of GeneGlobe Pathway Central Maps for RNU1-2

Spliceosomal Splicing Cycle

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Interactions:

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(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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(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,
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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5/7 fRNAdb Secondary structures (see all 7):

1 Ensembl transcript including schematic representation, and UCSC links where relevant:

ENST00000384278(snRNA)

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GeneLoc Exon Structure

(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 RNU1-2:none

See probesets specificity/sensitivity at GeneAnnot
CGAP TAG: --

RNU1-2 Protein expression data from MOPED¹, PaxDb² and MaxQB³:

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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)
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This gene was present in the common ancestor of mammals.

Orthologs for RNU1-2 gene from Selected species (see all 3) About this table

Organism	Taxonomic classification	Gene	Description	Human Similarity	Orthology Type	Details
dog (Canis familiaris)	Mammalia	U1⁶	U1 spliceosomal RNA	99(a)	1 → many	18(50902588-50902751) ENSCAFG00000030934

ENSEMBL Gene Tree for RNU1-2 (if available)
TreeFam Gene Tree for RNU1-2 (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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SNP ID	Valid	Clinical significance	Chr 1 pos	Sequence	#	AA Chg	Type	More	#	Allele freq	Pop	Total sample	More
Genomic Data					Transcription Related Data				Allele Frequencies
				--	--	--		--	--
rs11203349^1,2	C,F,A,H	--	17220490(+)	`gattgC/Gtttga`	1	--	us2k¹		5		NA CSA	12
rs7418159^1,2	C,F	--	17220522(+)	`atgtcG/Atggct`	1	--	us2k¹		3		NA WA	122
rs11203350^1,2	C,F,A,H	--	17220539(+)	`tgtcaG/Atgaaa`	1	--	us2k¹		4		NA CSA	9
rs7418181^1,2	C,H	--	17220614(+)	`catcaG/Cgtagt`	1	--	us2k¹		6		NS EA NA	416
rs200575807^1,2	C	--	17220652(+)	`TCCACA/GAAGGC`	1	--	us2k¹		0	--	--	--	--
rs144089201^1,2		--	17220665(+)	`GTCAGA/TTACCC`	1	--	us2k¹		0	--	--	--	--
rs7366350^1,2	C,F,A,H	--	17220670(+)	`ATACCC/TAGAAA`	1	--	us2k¹		4		NA WA	10
rs147418674^1,2	C	--	17220704(+)	`CAATGG/TGTCTC`	1	--	us2k¹		0	--	--	--	--
rs7418582^1,2	C	--	17220724(+)	`CTCCAG/AGGAAT`	1	--	us2k¹ tfbs³		2		NA	4
rs369962417^1,2	C	--	17220738(+)	`GCCTGA/GTCAAG`	1	--	us2k¹		0	--	--	--	--

HapMap Linkage Disequilibrium report for RNU1-2 (17222475 - 17222638 bp)

Structural Variations
Database of Genomic Variants (DGV) variations for RNU1-2: --

Site Specific Mutation Identification with 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.)
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(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 RNU1-2 gene integrated from 10 sources:
(articles sorted by number of sources associating them with RNU1-2)

Utopia: connect your pdf to the dynamic
world of online information

Human U1 small nuclear RNA genes: extensive conservation of flanking sequences suggests cycles of gene amplification and transposition. (PubMed id 3837185)^{1, 3} Bernstein L.B....Weiner A.M. (Mol. Cell. Biol. 1985)
(PubMed id 8797828)¹⁰
(PubMed id 9016512)¹⁰
(PubMed id 2977088)¹⁰
(PubMed id 15608158)¹⁰
(PubMed id 2405391)¹⁰
(PubMed id 7984237)¹⁰
(PubMed id 11297556)¹⁰

(in PubMed, OMIM, and NCBI Bookshelf)
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		AND	OR
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: 26870	HGNC: 10123	Ensembl:ENSG00000207005	euGenes: HUgn26870	ECgene: RNU1-2
H-InvDB: RNU1-2

(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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Name	Description
PharmGKB entry for RNU1-2	Pharmacogenomics, SNPs, Pathways

Intellectual Property for RNU1-2 gene
(Patent information from GeneIP, Licensable technologies from WIS Yeda, Salk, Tufts, IP news from LifeMap Sciences, Inc.)

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Patent Information for RNU1-2 gene:
Search GeneIP for patents involving RNU1-2

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

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RNU1-2 Gene

RNA, U1 Small Nuclear 2

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RNU1-2 Gene

RNA, U1 Small Nuclear 2

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