Human Gene SNRPN (ENST00000400097.5) from GENCODE V44
  Description: Homo sapiens small nuclear ribonucleoprotein polypeptide N (SNRPN), transcript variant 2, mRNA. (from RefSeq NM_022805)
RefSeq Summary (NM_022805): This gene is located within the Prader-Willi Syndrome critical region on chromosome 15 and is imprinted and expressed from the paternal allele. It encodes a component of the small nuclear ribonucleoprotein complex, which functions in pre-mRNA processing and may contribute to tissue-specific alternative splicing. Alternative promoter use and alternative splicing result in a multitude of transcript variants encoding the same protein. Transcript variants that initiate at the CpG island-associated imprinting center may be bicistronic and also encode the SNRPN upstream reading frame protein (SNURF) from an upstream open reading frame. In addition, long spliced transcripts for small nucleolar RNA host gene 14 (SNHG14) may originate from the promoters at this locus and share exons with this gene. Alterations in this region are associated with parental imprint switch failure, which may cause Angelman syndrome or Prader-Willi syndrome. [provided by RefSeq, Mar 2017].
Gencode Transcript: ENST00000400097.5
Gencode Gene: ENSG00000128739.23
Transcript (Including UTRs)
   Position: hg38 chr15:24,856,551-24,978,582 Size: 122,032 Total Exon Count: 12 Strand: +
Coding Region
   Position: hg38 chr15:24,974,454-24,978,444 Size: 3,991 Coding Exon Count: 7 

Page IndexSequence and LinksPrimersMalaCardsCTDRNA-Seq Expression
Microarray ExpressionRNA StructureOther SpeciesmRNA DescriptionsOther NamesMethods
Data last updated at UCSC: 2023-08-18 00:09:47

-  Sequence and Links to Tools and Databases
Genomic Sequence (chr15:24,856,551-24,978,582)mRNA (may differ from genome)Protein (240 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGencodeGeneCards
UniProtKBWikipediaBioGrid CRISPR DB

-  Primer design for this transcript

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3

-  MalaCards Disease Associations
  MalaCards Gene Search: SNRPN
Diseases sorted by gene-association score: prader-willi syndrome* (397), autistic disorder* (52), autism spectrum disorder* (39), angelman syndrome (26), prader-willi syndrome due to translocation* (25), prader-willi syndrome due to imprinting mutation* (25), prader-willi syndrome due to maternal uniparental disomy of chromosome 15* (25), prader-willi syndrome due to paternal deletion of 15q11q13 type 1* (18), prader-willi syndrome due to paternal deletion of 15q11q13 type 2* (18), angelman syndrome due to imprinting defect in 15q11-q13* (18), chromosomal disease (4), systemic lupus erythematosus (3)
* = Manually curated disease association

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 7.14 RPKM in Brain - Nucleus accumbens (basal ganglia)
Total median expression: 108.73 RPKM

View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -227.20744-0.305 Picture PostScript Text
3' UTR -23.90138-0.173 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
Genome BrowserGenome BrowserNo orthologNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
Protein SequenceProtein Sequence    

-  Descriptions from all associated GenBank mRNAs
  L80005 - Homo sapiens u1B-IC/SNRPN transcript, mRNA sequence.
L80004 - Homo sapiens u1A-IC/SNRPN transcript, mRNA sequence.
AK222633 - Homo sapiens mRNA for small nuclear ribonucleoprotein polypeptide N variant, clone: CBL04839.
BC035280 - Homo sapiens, small nuclear ribonucleoprotein polypeptide N, clone IMAGE:5179670, mRNA.
JD564971 - Sequence 545995 from Patent EP1572962.
JD454342 - Sequence 435366 from Patent EP1572962.
JD171674 - Sequence 152698 from Patent EP1572962.
U41303 - Human small nuclear ribonuleoprotein particle N (SNRPN) mRNA, complete cds.
AF101044 - Homo sapiens SNRPN upstream reading frame protein (SNURF) mRNA, complete cds.
AK098563 - Homo sapiens cDNA FLJ25697 fis, clone TST04565, highly similar to SMALL NUCLEAR RIBONUCLEOPROTEIN ASSOCIATED PROTEIN N.
J04615 - Human lupus autoantigen (small nuclear ribonuclepoprotein, snRNP, SM-D) mRNA, complete cds.
BC000445 - Homo sapiens cDNA clone IMAGE:2820873, **** WARNING: chimeric clone ****.
BC018809 - Homo sapiens cDNA clone IMAGE:2820501.
BC010057 - Homo sapiens cDNA clone IMAGE:3945980, **** WARNING: chimeric clone ****.
BC003180 - Homo sapiens small nuclear ribonucleoprotein polypeptide N, mRNA (cDNA clone MGC:4420 IMAGE:2958068), complete cds.
BC063608 - Homo sapiens cDNA clone IMAGE:4940200, **** WARNING: chimeric clone ****.
BC025178 - Homo sapiens small nuclear ribonucleoprotein polypeptide N, mRNA (cDNA clone MGC:34180 IMAGE:4158469), complete cds.
AF319522 - Homo sapiens RT-LII mRNA, complete sequence.
AF319523 - Homo sapiens RT-LI mRNA, complete sequence.
AB590506 - Synthetic construct DNA, clone: pFN21AE1101, Homo sapiens SNURF gene for SNRPN upstream reading frame, without stop codon, in Flexi system.
BC024777 - Homo sapiens small nuclear ribonucleoprotein polypeptide N, mRNA (cDNA clone MGC:29886 IMAGE:3907606), complete cds.
BC113069 - Homo sapiens cDNA clone IMAGE:40024120, **** WARNING: chimeric clone ****.
DQ571397 - Homo sapiens piRNA piR-31509, complete sequence.
X15892 - Human hcerN3 gene mRNA for N snRNP associated protein.
JD106997 - Sequence 88021 from Patent EP1572962.
JD038469 - Sequence 19493 from Patent EP1572962.
JD237060 - Sequence 218084 from Patent EP1572962.
JD268292 - Sequence 249316 from Patent EP1572962.
AK123119 - Homo sapiens cDNA FLJ41124 fis, clone BRACE2014850, highly similar to Small nuclear ribonucleoprotein-associated protein N.
BC000611 - Homo sapiens small nuclear ribonucleoprotein polypeptide N, mRNA (cDNA clone MGC:1613 IMAGE:3347412), complete cds.
AF400432 - Homo sapiens small nuclear ribonucleoprotein polypeptide N (SNRPN) mRNA, complete cds.
DQ896135 - Synthetic construct Homo sapiens clone IMAGE:100010595; FLH190652.01L; RZPDo839C0866D small nuclear ribonucleoprotein polypeptide N (SNRPN) gene, encodes complete protein.
DQ892886 - Synthetic construct clone IMAGE:100005516; FLH190656.01X; RZPDo839C0876D small nuclear ribonucleoprotein polypeptide N (SNRPN) gene, encodes complete protein.
AB528328 - Synthetic construct DNA, clone: pF1KB0983, Homo sapiens SNRPN gene for small nuclear ribonucleoprotein polypeptide N, without stop codon, in Flexi system.
CR450350 - Homo sapiens full open reading frame cDNA clone RZPDo834H032D for gene SNRPN, small nuclear ribonucleoprotein polypeptide N; complete cds; without stopcodon.
KJ534946 - Homo sapiens clone SNRPN_iso-A_adult-A01 small nuclear ribonucleoprotein polypeptide N isoform A (SNRPN) mRNA, partial cds, alternatively spliced.
CU692934 - Synthetic construct Homo sapiens gateway clone IMAGE:100016860 5' read SNURF mRNA.
HQ447144 - Synthetic construct Homo sapiens clone IMAGE:100070432; CCSB003905_01 SNRPN upstream reading frame (SNURF) gene, encodes complete protein.
KJ892181 - Synthetic construct Homo sapiens clone ccsbBroadEn_01575 SNRPN gene, encodes complete protein.
JD450123 - Sequence 431147 from Patent EP1572962.
X16163 - Human mRNA for SmB/B' autoimmune antigene (K5-1).
JD452185 - Sequence 433209 from Patent EP1572962.
JD531125 - Sequence 512149 from Patent EP1572962.
JD440400 - Sequence 421424 from Patent EP1572962.
JD381859 - Sequence 362883 from Patent EP1572962.
JD431947 - Sequence 412971 from Patent EP1572962.
JD465871 - Sequence 446895 from Patent EP1572962.
JD225640 - Sequence 206664 from Patent EP1572962.
JD453020 - Sequence 434044 from Patent EP1572962.
JD547320 - Sequence 528344 from Patent EP1572962.
JD108258 - Sequence 89282 from Patent EP1572962.
JD346064 - Sequence 327088 from Patent EP1572962.
JD548723 - Sequence 529747 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: ENST00000400097.1, ENST00000400097.2, ENST00000400097.3, ENST00000400097.4, NM_022805, uc001ywt.1, X5DP00
UCSC ID: ENST00000400097.5
RefSeq Accession: NM_022805
CCDS: CCDS10017.1

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.