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SNRNP25 Gene

protein-coding   GIFtS: 41
GCID: GC16P000103

Small Nuclear Ribonucleoprotein 25kDa (U11/U12)

(Previous name: chromosome 16 open reading frame 33)
(Previous symbol: C16orf33)
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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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Aliases
Small Nuclear Ribonucleoprotein 25kDa (U11/U12)1 2     U11/U12 SnRNP 25 KDa Protein2 3
C16orf331 2 3     Chromosome 16 Open Reading Frame 331
U11/U12 SnRNP 25K1 2     U11/U12 Small Nuclear Ribonucleoprotein 25 KDa Protein2
Minus-99 Protein2 3     U11/U12-25K3

External Ids:    HGNC: 141611   Entrez Gene: 796222   Ensembl: ENSG000001619817   UniProtKB: Q9BV903   

Export aliases for SNRNP25 gene to outside databases

Previous GC identifers: GC16P000044 GC16P000022


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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Entrez Gene summary for SNRNP25 Gene:
Two types of spliceosomes catalyze splicing of pre-mRNAs. The major U2-type spliceosome is found in all eukaryotes
and removes U2-type introns, which represent more than 99% of pre-mRNA introns. The minor U12-type spliceosome is
found in some eukaryotes and removes U12-type introns, which are rare and have distinct splice consensus signals.
The U12-type spliceosome consists of several small nuclear RNAs and associated proteins. This gene encodes a 25K
protein that is a component of the U12-type spliceosome. (provided by RefSeq, Apr 2010)

GeneCards Summary for SNRNP25 Gene:
SNRNP25 (small nuclear ribonucleoprotein 25kDa (U11/U12)) is a protein-coding 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_000016.9  NC_018927.2  NT_010393.17  
Regulatory elements:
   Regulatory transcription factor binding sites in the SNRNP25 gene promoter:
         E2F-4   E2F-3a   STAT1   E2F-5   p53   STAT1beta   E2F-2   STAT1alpha   E2F   E2F-1   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmids (see all 2): SNRNP25 promoter sequence
   Search Chromatin IP Primers for SNRNP25

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat SNRNP25


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

Entrez Gene cytogenetic band: 16p13.3   Ensembl cytogenetic band:  16p13.3   HGNC cytogenetic band: 16p13.3

SNRNP25 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
SNRNP25 gene location

GeneLoc information about chromosome 16         GeneLoc Exon Structure

GeneLoc location for GC16P000103:  view genomic region     (about GC identifiers)

Start:
103,010 bp from pter      End:
107,669 bp from pter
Size:
4,660 bases      Orientation:
plus strand

(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/Swiss-Prot: SNR25_HUMAN, Q9BV90 (See protein sequence)
Recommended Name: U11/U12 small nuclear ribonucleoprotein 25 kDa protein  
Size: 132 amino acids; 15270 Da
Subunit: Component of the U11/U12 snRNPs that are part of the U12-type spliceosome
Caution: It is uncertain whether Met-1 or Met-10 is the initiator
Secondary accessions: Q1W6H3 Q6IEF8 Q9H5W4

Explore the universe of human proteins at neXtProt for SNRNP25: NX_Q9BV90

Explore proteomics data for SNRNP25 at MOPED


See SNRNP25 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

REFSEQ proteins: NP_078847.1  
ENSEMBL proteins: 
 ENSP00000293861   ENSP00000380974   ENSP00000391289   ENSP00000372482  

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(According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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1 InterPro protein domain:
 IPR000626 Ubiquitin_dom

Graphical View of Domain Structure for InterPro Entry Q9BV90

ProtoNet protein and cluster: Q9BV90

1 Blocks protein domain: IPB000626 Ubiquitin domain

UniProtKB/Swiss-Prot: SNR25_HUMAN, Q9BV90
Similarity: Contains 1 ubiquitin-like domain


Find genes that share domains with SNRNP25           About GenesLikeMe


(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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     Gene Ontology (GO): 1 molecular function term:    About this table

GO IDQualified GO termEvidencePubMed IDs
GO:0005515protein binding ----
     
Find genes that share ontologies with SNRNP25           About GenesLikeMe


Phenotypes:
     1 GenomeRNAi human phenotype for SNRNP25:
 Increased gamma-H2AX phosphory 

Animal Models:
   genOway: Develop your customized and physiologically relevant rodent model for SNRNP25

miRNA
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hsa-miR-4318
SwitchGear 3'UTR luciferase reporter plasmidSNRNP25 3' UTR sequence
Inhib. RNA
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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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Subcellular locations from UniProtKB/Swiss-Prot
SNR25_HUMAN, Q9BV90: Nucleus
Subcellular locations from COMPARTMENTS: 

CompartmentConfidence
nucleus5
cytosol2
mitochondrion1

Gene Ontology (GO): 5 cellular component terms:    About this table

GO IDQualified GO termEvidencePubMed IDs
GO:0005634nucleus IDA--
GO:0005689U12-type spliceosomal complex IDA15146077
GO:0005730NOT nucleolus IDA--
GO:0005737cytoplasm IDA--
GO:0045171intercellular bridge IDA--

Find genes that share ontologies with SNRNP25           About GenesLikeMe


(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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Interactions:

    Search GeneGlobe Interaction Network for SNRNP25

Gene Ontology (GO): 2 biological process terms:    About this table

GO IDQualified GO termEvidencePubMed IDs
GO:0006397mRNA processing IEA--
GO:0008380RNA splicing IC15146077

Find genes that share ontologies with SNRNP25           About GenesLikeMe



(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 SNRNP25 (SNR25)



(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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REFSEQ mRNAs for SNRNP25 gene: 
NM_024571.3  

Unigene Cluster for SNRNP25:

Small nuclear ribonucleoprotein 25kDa (U11/U12)
Hs.15277  [show with all ESTs]
Unigene Representative Sequence: BC001381
7 Ensembl transcripts including schematic representations, and UCSC links where relevant:
ENST00000293861(uc002cfj.4) ENST00000397876 ENST00000493672 ENST00000417493
ENST00000466183 ENST00000481947 ENST00000383018
miRNA
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hsa-miR-4318
SwitchGear 3'UTR luciferase reporter plasmidSNRNP25 3' UTR sequence
Inhib. RNA
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Primer
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  QuantiFast Probe-based Assays in human, mouse, rat SNRNP25

Additional mRNA sequence: 

AK026593.1 BC001381.1 BC009179.1 Z84714.1 

7 DOTS entries:

DT.213827  DT.213826  DT.95275307  DT.100861693  DT.120670922  DT.99935488  DT.40108600 

Selected AceView cDNA sequences (see all 182):

BU846188 AA335786 BM794653 CR620069 CR594984 BM712091 BM006127 BM691420 
CR609842 CR590942 BQ222254 CR613103 BQ686053 BU521371 AI820975 BG166061 
AJ708079 BQ057117 AI742126 BU508290 AW007372 AJ346502 AA613023 CB139779 

GeneLoc Exon Structure

2 Alternative Splicing Database (ASD) splice patterns (SP) for SNRNP25    About this scheme

ExUns: 1a · 1b ^ 2 ^ 3 ^ 4 ^ 5 ^ 6a · 6b
SP1:                                                
SP2:                          -                     


ECgene alternative splicing isoforms for SNRNP25

(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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SNRNP25 expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS <intensity>2/3
CGAP TAG: GCAGACCCAC
SNRNP25 Expression
About this image

SNRNP25 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

SNRNP25 Protein Expression

SOURCE GeneReport for Unigene cluster: Hs.15277
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In Situ
Assay Products:
 

 
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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 eukaryotes.

Orthologs for SNRNP25 gene from Selected species (see all 13)    About this table
Organism Taxonomic
classification
Gene Description Human
Similarity
Orthology
Type
Details
mouse
(Mus musculus)
Mammalia Snrnp251 , 5 small nuclear ribonucleoprotein 25 (U11/U12)1, 5 88.35(n)1
98.37(a)1
  11 (18.82 cM)5
783721  NM_030093.31  NP_084369.21 
 322054155 
chicken
(Gallus gallus)
Aves C16ORF331 small nuclear ribonucleoprotein 25kDa (U11/U12) 73.54(n)
76.34(a)
  425933  XM_004945346.1  XP_004945403.1 
lizard
(Anolis carolinensis)
Reptilia SNRNP256
small nuclear ribonucleoprotein 25kDa (U11/U12)
62(a)
1 ↔ 1
GL343856.1(158132-163701)
African clawed frog
(Xenopus laevis)
Amphibia MGC685202 hypothetical protein MGC68520 74.32(n)    BC060402.1 
zebrafish
(Danio rerio)
Actinopterygii snrnp251 small nuclear ribonucleoprotein 25 70.45(n)
78.79(a)
  550385  NM_001017690.1  NP_001017690.1 
thale cress
(Arabidopsis thaliana)
eudicotyledons AT3G078601 AT3G07860 46.5(n)
40.34(a)
  819977  NM_111665.2  NP_187443.2 


ENSEMBL Gene Tree for SNRNP25 (if available)
TreeFam Gene Tree for SNRNP25 (if available)

(Paralogs according to 1HomoloGene,
2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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Paralogs for SNRNP25 gene
1 SIMAP similar gene for SNRNP25 using alignment to 2 protein entries:     SNR25_HUMAN (see all proteins):
C16orf33

Find genes that share paralogs with SNRNP25           About GenesLikeMe



(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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Selected SNPs for SNRNP25 (see all 183)    About this table                                 

Genomic DataTranscription Related DataAllele Frequencies
SNP IDValidClinical
significance
Chr 16 posSequence#AA
Chg
TypeMore#Allele
freq
PopTotal
sample
More
----------
rs1917981981,2
--41816(+) CAAGAA/GATCGA 1 -- us2k10--------
rs2165911,2
C,F--41939(+) aatggC/Tgtgaa 1 -- us2k11Minor allele frequency- T:0.50CSA 2
rs1832002711,2
--41955(+) GAGGCA/GGAGCT 1 -- us2k10--------
rs2165921,2
C,F,H--41978(+) agatcG/Acacca 1 -- us2k19Minor allele frequency- A:0.10NA WA CSA 20
rs1435887251,2
--42061(+) CGTAGC/TTTCAA 1 -- us2k10--------
rs1878137491,2
--42177(+) AGGCGC/TGGTGG 1 -- us2k10--------
rs1480554181,2
--42187(+) GCTCAC/GGCCTA 1 -- us2k10--------
rs1911737131,2
--42205(+) AGCACC/TTTGGG 1 -- us2k10--------
rs1834486241,2
--42277(+) AAACCA/CCGTCT 1 -- us2k10--------
rs2165931,2
C--42468(+) AAAggA/Tcgggc 1 -- us2k11Minor allele frequency- T:0.00NA 2

HapMap Linkage Disequilibrium report for SNRNP25 (103010 - 107669 bp)

Structural Variations
     Database of Genomic Variants (DGV) 9 variations for SNRNP25:    About this table    
Variant IDTypeSubtypePubMed ID
esv988339CNV Deletion20482838
esv2422427CNV Duplication17116639
nsv904628CNV Loss21882294
nsv522688CNV Loss19592680
nsv518291CNV Loss19592680
dgv2456n71CNV Loss21882294
dgv2455n71CNV Loss21882294
nsv904623CNV Gain+Loss21882294
dgv789e1CNV Complex17122850

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(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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  --

(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 SNRNP25 gene integrated from 10 sources:
(articles sorted by number of sources associating them with SNRNP25)
    Utopia: connect your pdf to the dynamic
world of online information

  1. The human 18S U11/U12 snRNP contains a set of novel proteins not found in the U2-dependent spliceosome. (PubMed id 15146077)1, 2, 3 Will C.L.... Luehrmann R. (RNA 2004)
  2. A regulatory SNP causes a human genetic disease by creating a new transcriptional promoter. (PubMed id 16728641)1, 2 De Gobbi M.... Higgs D.R. (Science 2006)
  3. The sequence and analysis of duplication-rich human chromosome 16. (PubMed id 15616553)1, 2 Martin J.... Pennacchio L.A. (Nature 2004)
  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. (Genome Res. 2004)
  5. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1, 2 Ota T.... Sugano S. (Nat. Genet. 2004)
  6. Why do cellular proteins linked to K63-polyubiquitin chains not associate with proteasomes? (PubMed id 23314748)1 Nathan J.A....Goldberg A.L. (EMBO J. 2013)
  7. Pathway Analysis of ChIP-Seq-Based NRF1 Target Genes Suggests a Logical Hypothesis of their Involvement in the Pathogenesis of Neurodegenerative Diseases. (PubMed id 24250222)1 Satoh J....Yamamoto Y. (Gene Regul Syst Bio 2013)
  8. Minor spliceosome components are predominantly localized in the nucleus. (PubMed id 18559850)1 Pessa H.K....Frilander M.J. (Proc. Natl. Acad. Sci. U.S.A. 2008)
  9. 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. (Proc. Natl. Acad. Sci. U.S.A. 2002)

(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)

(According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
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Entrez Gene: 79622 HGNC: 14161 AceView: C16orf33 Ensembl:ENSG00000161981 euGenes: HUgn79622
ECgene: SNRNP25 H-InvDB: SNRNP25

(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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NameDescription
PharmGKB entry for SNRNP25 Pharmacogenomics, SNPs, Pathways

(Patent information from GeneIP,
Licensable technologies from WIS Yeda, Salk, Tufts,
IP news from LifeMap Sciences, Inc.)
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Patent Information for SNRNP25 gene:
Search GeneIP for patents involving SNRNP25

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, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Cloud-Clone Corp., Thermo Fisher Scientific, eBioscience, antibodies-online, and/or others, Gene Editing from DNA2.0. Clones from OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Addgene, Cell lines from GenScript, and ESI BIO, Flow cytometery from eBioscience, PCR Arrays from QIAGEN, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, Enzo Life Sciences, and/or ApexBio, In Situ Hybridization Assays from
Advanced Cell Diagnostics, Animal models from genOway)
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 Novus Tissue Slides
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GeneCards Homepage - Last full update: 7 May 2014 - Incrementals: 9 May 2014 , 2 Jun 2014 , 26 Jun 2014 , 30 Jun 2014 , 21 Aug 2014 , 8 Sep 2014 , 7 Oct 2014

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