HsaINT0132640 @ hg38
Intron Retention
Gene
ENSG00000196504 | PRPF40A
Description
pre-mRNA processing factor 40 homolog A [Source:HGNC Symbol;Acc:HGNC:16463]
Coordinates
chr2:152679352-152681336:-
Coord C1 exon
chr2:152681226-152681336
Coord A exon
chr2:152679473-152681225
Coord C2 exon
chr2:152679352-152679472
Length
1753 bp
Sequences
Splice sites
5' ss Seq
GAGGTAAAA
5' ss Score
7.3
3' ss Seq
AACAGTTTTTTCCTTTTCAGCAA
3' ss Score
8.53
Exon sequences
Seq C1 exon
AAATCAATGTGGACTGAACATAAATCACCTGATGGAAGGACTTACTACTACAACACTGAAACCAAACAGTCTACCTGGGAGAAACCAGATGATCTTAAAACACCTGCTGAG
Seq A exon
GTAAAAGTTTGAGAGCTGGAATTCAGGGACTGTCAAGTAGACTGGGGCGTATTTTTTAGGATTCTATAAGTAGTCGATTATCAAAGAGCAGTACTGCTTAAATGTCAGAAGAGGATCTGTAAAGACATTCAGAAAAAAAGAGGGTTAGTATAGTCACACCAATCGGGAAGAAGAGCAATAAAACTCAACAGAATAATTTTATTTACTGATTTTACCCCTGCTTAGAAAACCTAGTAGAGTGGGATCAATTTTAAAAAGGTGATTTAAAGAATAAATTGGAAGTGGGGAAGACTGTTTCTTTGCCTGCCGCTGGCTTTTTTTTCTGATAGCAAAACTGGGTGATTTTAAATGACTTCTACTGAGTTCTTAAATTTCCAGTAGGGTTAAGGGTAGTGGAGATGAAATTAAGTTACCTACAAATACTTCCTTCTCTTAGAGTGGGAAGTTTTCTCTTTGCAGGAAATGCCCTTTTAAAAAGTGTGTTTTTATTTTGTTTTTTGTTACAAGTTTTACCATTCAAAATATACAGATATTGAAGAAAAAGTTAAGGTTGAAGGAATAAACTGAATTAAGCAATGTCACATGTTGTTTAATTAGAAACTCTGGGGTGCTAAGTAAGTAAGAGTTGATCTGGCACTCCAGGCTATGCTTAAGTTTCATCCTAGCTGGTGGTATACCTTTTTGTTTTCTTCTCTTCCTAATTAAGGAATTTGAGAAGGTAAAAGTATTTTCCAGGTTGCTGTACTAACATGAACAGCAGTGCTTGGGAGGGGAGGTCGGACGATTTTTAAAAACATGTATTCCAGTACTGATTTATAGCCAATGATATTAATTACATACTTTGTCCAAGACACTCTGTTTGGATTCACACTTTGAATAGATTTCTCATACTACCCTAACAGGTTTTGTTTATTCGATTTTAAGTATATTATACCTACATGTTTTCTTACATAATAAGTTAATTCGTTCATAAACTACGAAACTGAAATCTAAGCATGACTAAATTAGATTTTGTTTTTTTTGAACTTTTATGGTTTTCCAACTAATATTAGTATCAGAGAAGTCTGTTAAATGTGGATGATAGGCCGGGCGCGGTGGCTCACACTTGTAATCCCAGCACTTTGGGAGGCCGAGGCGGGCGGATCACGAGGTCAGGAGTTCGAGACCACGGTGAAACCCCGTCTCTACTAAAAAAAAATACAAAAAATTAGCTGGGCGTGGTGGCGGGCGCCTGTAGTCCCAGCTACTCAGAGAGGCTGAGGCAGGAGAATGGCGTGAACCCGAGAGGCGGAGCTTGCAGTGAGCCGAGGTCGAGCTACTGTACTCCAGCCTGGGTGACAAAGCGAGACTCCGTCTCAAAAAAAAAAAAAAAAAAAAATGTGGATGATAATCTTGACCTATAATGGGGTGTGAATGGTTACAGTAAATAGGATTTGAAATTCATATAGAACTGGTTTTGAATCTTGTCTCTGCTTTTTAATGAGTATATTACCTTAAACAAGTTACTTTCTGACTTCAAGTAACAGTCCCTAGATACAGAATTATGTTACACATTTTGCAGTGTTATAAAGATTAAATAATGTATTCAAATGGCATCACTCAGTGAATATTCAATAATTGATAGTTTATATTATTACCATCATCTCACGAGTTTTAGAATTGTATCAATTGGTAATTTCTAGTGAAAACAGCCATGTAAATGATCAGTGATGTTAAATATATTATTATTAACAAACAGTTTTTTCCTTTTCAG
Seq C2 exon
CAACTCTTATCTAAATGCCCCTGGAAGGAATACAAATCAGATTCTGGAAAGCCTTACTATTATAATTCTCAAACAAAAGAATCTCGCTGGGCCAAACCTAAAGAACTTGAGGATCTTGAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000196504:ENST00000410080:6
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.816 A=NA C2=0.524
Domain overlap (PFAM):
C1:
PF0039721=WW=PD(93.3=75.7)
A:
NA
C2:
PF0039721=WW=WD(100=73.2)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
ATCAATGTGGACTGAACATAAATCAC
R:
CTTCAAGATCCTCAAGTTCTTTAGGT
Band lengths:
230-1983
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Autistic and control brains
- Pre-implantation embryo development