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SNRNP48 Gene

protein-coding   GIFtS: 46
GCID: GC06P007590

Small Nuclear Ribonucleoprotein 48kDa (U11/U12)

(Previous name: chromosome 6 open reading frame 151)
(Previous symbol: C6orf151)
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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 48kDa (U11/U12)1 2     Chromosome 6 Open Reading Frame 1511
C6orf1511 2 3     dJ336K20B.12
U11/U12 SnRNP 48K1 2     dJ512B11.22
U11/U12-48K2 3     U11/U12 Small Nuclear Ribonucleoprotein 48 KDa Protein2
U11/U12 SnRNP 48 KDa Protein2 3     

External Ids:    HGNC: 213681   Entrez Gene: 1540072   Ensembl: ENSG000001685667   UniProtKB: Q6IEG03   

Export aliases for SNRNP48 gene to outside databases

Previous GC identifers: GC06P007536 GC06P007467


(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 SNRNP48 Gene:
SNRNP48 (small nuclear ribonucleoprotein 48kDa (U11/U12)) is a protein-coding gene.

UniProtKB/Swiss-Prot: SNR48_HUMAN, Q6IEG0
Function: Likely involved in U12-type 5' splice site recognition




(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_000006.11  NT_007592.16  NC_018917.2  
Regulatory elements:
   Regulatory transcription factor binding sites in the SNRNP48 gene promoter:
         ER-alpha   E2F-4   E2F-3a   E2F-5   Nkx2-5   E2F-2   FOXL1   AREB6   E2F   E2F-1   
         Other transcription factors

Browse SwitchGear Promoter luciferase reporter plasmids
   Search Chromatin IP Primers for SNRNP48

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat SNRNP48


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

Entrez Gene cytogenetic band: 6p24.3   Ensembl cytogenetic band:  6p24.3   HGNC cytogenetic band: 6p24.3

SNRNP48 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
SNRNP48 gene location

GeneLoc information about chromosome 6         GeneLoc Exon Structure

GeneLoc location for GC06P007590:  view genomic region     (about GC identifiers)

Start:
7,590,432 bp from pter      End:
7,612,200 bp from pter
Size:
21,769 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: SNR48_HUMAN, Q6IEG0 (See protein sequence)
Recommended Name: U11/U12 small nuclear ribonucleoprotein 48 kDa protein  
Size: 339 amino acids; 39965 Da
Subunit: Component of the U11/U12 snRNPs that are part of the U12-type spliceosome. Not found in the major
spliceosome
2 PDB 3D structures from and Proteopedia for SNRNP48:
2VY4 (3D)        2VY5 (3D)    
Secondary accessions: A8K8P4 Q14C91 Q5T339 Q5THM1 Q5THM2 Q96MK1
Alternative splicing: 2 isoforms:  Q6IEG0-1   Q6IEG0-2   (No experimental confirmation available)

Explore the universe of human proteins at neXtProt for SNRNP48: NX_Q6IEG0

Explore proteomics data for SNRNP48 at MOPED

Post-translational modifications: 

  • Ubiquitination2 at Lys128
  • Modification sites at PhosphoSitePlus

  • See SNRNP48 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins: NP_689764.3  
    ENSEMBL proteins: 
     ENSP00000339834  

    SNRNP48 Human Recombinant Protein Products:

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    Cloud-Clone Corp. Proteins for SNRNP48

     
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    antibodies-online proteins for SNRNP48 (2 products) 

     
    Search antibodies-online for peptides for SNRNP48

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    antibodies-online antibodies for SNRNP48 (8 products) 

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    antibodies-online kits for SNRNP48 (4 products) 


    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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    2 InterPro protein domains:
     IPR007917 UPF0224
     IPR022776 TRM13/UPF0224_CHHC_Znf_dom

    Graphical View of Domain Structure for InterPro Entry Q6IEG0

    ProtoNet protein and cluster: Q6IEG0

    UniProtKB/Swiss-Prot: SNR48_HUMAN, Q6IEG0
    Domain: The CHHC region interacts with the 5' splice site of the U12-type intron
    Similarity: Contains 1 CHHC-type zinc finger


    Find genes that share domains with SNRNP48           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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    Molecular Function:

         UniProtKB/Swiss-Prot Summary: SNR48_HUMAN, Q6IEG0
    Function: Likely involved in U12-type 5' splice site recognition

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

    GO IDQualified GO termEvidencePubMed IDs
    GO:0046872metal ion binding IEA--
         
    Find genes that share ontologies with SNRNP48           About GenesLikeMe


    Animal Models:
       genOway: Develop your customized and physiologically relevant rodent model for SNRNP48

    miRNA
    Products:
        
    miRTarBase miRNAs that target SNRNP48:
    hsa-mir-320a (MIRT044542), hsa-mir-21-5p (MIRT030727)

    Block miRNA regulation of human, mouse, rat SNRNP48 using miScript Target Protectors
    8 qRT-PCR Assays for microRNAs that regulate SNRNP48:
    hsa-miR-579 hsa-miR-3133 hsa-miR-570 hsa-miR-144 hsa-miR-186 hsa-miR-9* hsa-miR-3143 hsa-miR-145
    SwitchGear 3'UTR luciferase reporter plasmidSNRNP48 3' UTR sequence
    Inhib. RNA
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    Predesigned siRNA for gene silencing in human, mouse, rat SNRNP48

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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
    SNR48_HUMAN, Q6IEG0: Nucleus
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    nucleus5
    cytosol3
    extracellular1
    plasma membrane1

    Gene Ontology (GO): 3 cellular component terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005634nucleus ----
    GO:0005689U12-type spliceosomal complex IDA15146077
    GO:0005737cytoplasm ----

    Find genes that share ontologies with SNRNP48           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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        Custom Pathway & Disease-focused RT2 Profiler PCR Arrays for SNRNP48
    Interactions:

        Search GeneGlobe Interaction Network for SNRNP48

    STRING Interaction Network Preview (showing 2 interactants - click image to see more details)

    2 Interacting proteins for SNRNP48 (ENSP000003398344) via UniProtKB, MINT, STRING, and/or I2D
    InteractantInteraction Details
    GeneCardExternal ID(s)
    ELAVL1ENSP000003852694STRING: ENSP00000385269
    UBCENSP000003448184STRING: ENSP00000344818
    About this table

    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 SNRNP48           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 Small Molecules at EMD Millipore
       Browse drugs & compounds from Enzo Life Sciences
      Browse compounds at ApexBio 

    Browse Tocris compounds for SNRNP48 (SNR48)



    (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 SNRNP48 gene: 
    NM_152551.3  

    Unigene Cluster for SNRNP48:

    Small nuclear ribonucleoprotein 48kDa (U11/U12)
    Hs.13366  [show with all ESTs]
    Unigene Representative Sequence: NM_152551
    2 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000342415(uc003mxr.3 uc003mxs.3) ENST00000496946(uc003mxt.1)

    miRNA
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    8 qRT-PCR Assays for microRNAs that regulate SNRNP48:
    hsa-miR-579 hsa-miR-3133 hsa-miR-570 hsa-miR-144 hsa-miR-186 hsa-miR-9* hsa-miR-3143 hsa-miR-145
    SwitchGear 3'UTR luciferase reporter plasmidSNRNP48 3' UTR sequence
    Inhib. RNA
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    Predesigned siRNA for gene silencing in human, mouse, rat SNRNP48
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    Primer
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      QuantiTect SYBR Green Assays in human, mouse, rat SNRNP48
      QuantiFast Probe-based Assays in human, mouse, rat SNRNP48

    Additional mRNA sequence: 

    AJ420586.1 AK027220.1 AK056796.1 AK292409.1 AL832462.1 BC001558.1 BC054008.1 BC062458.1 
    BC114630.1 BC114631.1 

    6 DOTS entries:

    DT.442667  DT.100728279  DT.86842178  DT.95358188  DT.121322230  DT.100783429 

    Selected AceView cDNA sequences (see all 95):

    AI174594 CA437416 AI247204 AA814994 CR617787 AK056796 Z45200 Z45962 
    BC001558 AA659820 AI635052 AA815177 BQ881931 BQ066346 AI439404 AA630674 
    BF516050 AW768530 CD239130 AW964133 CB128938 NM_152551 AL526959 BM464200 

    GeneLoc Exon Structure

    5 Alternative Splicing Database (ASD) splice patterns (SP) for SNRNP48    About this scheme

    ExUns: 1a · 1b ^ 2 ^ 3 ^ 4 ^ 5 ^ 6a · 6b · 6c · 6d ^ 7a · 7b ^ 8 ^ 9a · 9b ^ 10 ^ 11
    SP1:                                -                                                     -     -         
    SP2:                                -     -                                                               
    SP3:                                                                                                      
    SP4:                                                                                                      
    SP5:                                                                                      -               


    ECgene alternative splicing isoforms for SNRNP48

    (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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    SNRNP48 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: AATGTTTAAC
    SNRNP48 Expression
    About this image

    SNRNP48 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    SNRNP48 Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.13366
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    In Situ
    Assay Products:
     

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for SNRNP48

    (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 SNRNP48 gene from Selected species (see all 12)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Snrnp481 , 5 small nuclear ribonucleoprotein 48 (U11/U12)1, 5 86.55(n)1
    86.35(a)1
      13 (18.04 cM)5
    677971  NM_026382.21  NP_080658.21 
     382049395 
    chicken
    (Gallus gallus)
    Aves SNRNP481 small nuclear ribonucleoprotein 48kDa (U11/U12) 69.68(n)
    69.68(a)
      420925  XM_419010.3  XP_419010.3 
    lizard
    (Anolis carolinensis)
    Reptilia SNRNP486
    small nuclear ribonucleoprotein 48kDa (U11/U12)
    62(a)
    1 ↔ 1
    4(66560017-66574098)
    African clawed frog
    (Xenopus laevis)
    Amphibia Xl.150022 Xenopus laevis transcribed sequence with weak similarity more 81.55(n)    BJ083172.1 
    zebrafish
    (Danio rerio)
    Actinopterygii wufd10a062 Danio rerio, clone IMAGE5604716, mRNA, partial cds 70.63(n)    BC049012.1 


    ENSEMBL Gene Tree for SNRNP48 (if available)
    TreeFam Gene Tree for SNRNP48 (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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    Selected SNPs for SNRNP48 (see all 443)    About this table                                 

    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 6 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs1925558051,2
    --7588451(+) ACAGGA/GAAATA 1 -- us2k10--------
    rs95052341,2
    C,F,H--7588506(+) TCTCAC/AATTTT 1 -- us2k121Minor allele frequency- A:0.26NS EA NA WA 2484
    rs1843595581,2
    --7588649(+) ACCAGC/TCTGGC 1 -- us2k10--------
    rs94060411,2
    C,F,H--7588821(+) CTGGGC/TGGCAG 1 -- us2k16Minor allele frequency- T:0.36NA WA CSA 11
    rs715428731,2
    C--7588842(+) GTCTC-/AAAAAA 1 -- us2k11Minor allele frequency- A:0.50NA 2
    rs1889378901,2
    C--7589035(+) AGTTCC/TTTCAC 1 -- us2k10--------
    rs1931128091,2
    --7589153(+) GGAAAC/GTACAA 1 -- us2k10--------
    rs27443821,2
    C,F,A,H--7589235(+) AGGACT/CAATAG 1 -- us2k126Minor allele frequency- C:0.21NS EA NA WA CSA 2772
    rs1844630561,2
    --7589302(+) AATTTC/GAGCAT 1 -- us2k10--------
    rs1479882201,2
    C--7589358(+) AAAAAA/CCCTTA 1 -- us2k10--------

    HapMap Linkage Disequilibrium report for SNRNP48 (7590432 - 7612200 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 8 variations for SNRNP48:    About this table    
    Variant IDTypeSubtypePubMed ID
    nsv5191CNV Insertion18451855
    nsv5189CNV Insertion18451855
    dgv370n21CNV Loss19592680
    nsv462624CNV Loss19166990
    nsv5190CNV Loss18451855
    nsv883433CNV Gain21882294
    nsv819694CNV Gain19587683
    nsv830580CNV Gain17160897

    Site Specific Mutation Identification with PCR Assays
    SeqTarget long-range PCR primers for resequencing SNRNP48
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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 SNRNP48 gene, integrated from 10 sources (see all 13):
    (articles sorted by number of sources associating them with SNRNP48)
        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. Solution structure of the U11-48K CHHC zinc-finger domain that specifically binds the 5' splice site of U12-type introns. (PubMed id 19217400)1, 2 Tidow H.... Fersht A.R. (Structure 2009)
    3. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1, 2 Ota T.... Sugano S. (Nat. Genet. 2004)
    4. The DNA sequence and analysis of human chromosome 6. (PubMed id 14574404)1, 2 Mungall A.J.... Beck S. (Nature 2003)
    5. Novel genetic loci identified for the pathophysiology of childhood obesity in the Hispanic population. (PubMed id 23251661)1 Comuzzie A.G....Butte N.F. (PLoS ONE 2012)
    6. Systematic and quantitative assessment of the ubiquitin-modified proteome. (PubMed id 21906983)1 Kim W....Gygi S.P. (Mol. Cell 2011)
    7. Ubiquitin-mediated proteolysis of HuR by heat shock. (PubMed id 19322201)1 Abdelmohsen K....Gorospe M. (EMBO J. 2009)
    8. A novel CHHC Zn-finger domain found in spliceosomal proteins and tRNA modifying enzymes. (PubMed id 18703587)2 Andreeva A. and Tidow H. (Bioinformatics 2008)
    9. Toward a confocal subcellular atlas of the human proteome. (PubMed id 18029348)1 Barbe L....Andersson-Svahn H. (amp 2008)
    10. The U11-48K protein contacts the 5' splice site of U12-type introns and the U11-59K protein. (PubMed id 18347052)1 Turunen J.J....Frilander M.J. (Mol. Cell. Biol. 2008)

    (in PubMed, OMIM, and NCBI Bookshelf)
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    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
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    Entrez Gene: 154007 HGNC: 21368 AceView: C6orf151 Ensembl:ENSG00000168566 euGenes: HUgn154007
    ECgene: SNRNP48 H-InvDB: SNRNP48

    (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 SNRNP48 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 SNRNP48 gene:
    Search GeneIP for patents involving SNRNP48

    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
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