DreINT0120528 @ danRer10
Intron Retention
Gene
ENSDARG00000058467 | prpf40a
Description
PRP40 pre-mRNA processing factor 40 homolog A (S. cerevisiae) [Source:ZFIN;Acc:ZDB-GENE-030131-274]
Coordinates
chr9:4743858-4746040:+
Coord C1 exon
chr9:4743858-4743995
Coord A exon
chr9:4743996-4745944
Coord C2 exon
chr9:4745945-4746040
Length
1949 bp
Sequences
Splice sites
5' ss Seq
GGAGTATGT
5' ss Score
4.82
3' ss Seq
TGTGTATTATGCTGGGTCAGGTA
3' ss Score
4.96
Exon sequences
Seq C1 exon
TTGCTCGAGAAGGCTGAAGCACGAGAGCGGGAGAGAGAAAAAGAGGAGGCCAGAAAGATGAAGAGGAAGGAAGCGGCGTTTAAGAGCATGTTAAAACAGGCCACACCCCCTCTAGAGCCCGAGGCCACGTGGGAGGGA
Seq A exon
GTATGTCACACTTTACATTACTATACAACAGTTTCATACAGGGGTGCACATAAGATAAGATGCGCAGCTAGAGAAGTACTTTTCTGTACCCGATTTCATAAATTTCACAGATTTTTCCAAATTTTCGGCTGCTGAGAATTATCATCTAATAAGGGCATTTATGGGTTCCTGTTGAAAAATAAAAATATGAGTAAAATTCAGTGACCATTTTCAGAGAAAAATACTAGATGTAGAAAGCAAAGTAGCTTAGTATTTGGCTCTGTAGATCTCACAGCCGCATGATAACATGTCATCACTGTAATTGTTCTTCAGTGTGTAACAGCAGCACTATGTTTGTCATTTGGTATCATGATTGCCTTAGTTGTTTACTATTGCGTCATATTACACACCCTGCCATTCAAACTGAACCGCTCCATGTCAGGTAAAGTAACTTACAAAGAAGAGCTGCCTCTCTTGTCTTTCACTGTTCAGCAGCAGAAGTGCAAAAACATATCAACAGGGATTGTTTTCCCTTAGCTTGAAACGACCACTAGCATAGTTAACCGACAGCAAGAATGGTGACAGACATCATGGTTAGAATGTAATTGAGATCATTATTGATTGTATTAAAAATATGCGTGAGTAAAGAATTCTACTAAATAGTCATGATTAAATTGTCAGCAAATGTTTTTTGTTTAGATATATCAATAAATATCTAAATAACAGTATCTCTAAATAACAATACAAATCTTAAAGCAGTAAAATTATAACCAAAAAAAGTTGAAGTCCGTGGAAAATTAAACCTTTTCCTGGTGATGTTGCAGTTTGGGGAATACTATTAATTTAATAATGTATTTTTTTTTTTTTTACAATTTAAAATGTTGAAAACTTTTATTTGAGTTTATTTTTTAAATCTGTACAAAAAAAAAAAAAAAACAGTAATTGGTCTTGACAAGACACACTTAACTTAATACAAGAAATTGAAATCGGCCAAGAAAATTGTAAAAAAAAAAGTAATAATTAATTATAACAGCATTTTCTTTTTCGAGTGCATCAGGAATTTTTATTTTTGGCTCAATTTTAATTTTGGTGCATACTTATTTAATTTTGCTGCGATTCAAATTGCGCAGCTCATAGCACTGTATGTAGACTCTTATTTGGAAGAAGAATGTAAAATAAAGTTGGTCTCTGTGGGCATGGATGGAGTTGCTGCGCTTGCAACAACATGTGTATCATGATATGTGTTCCTATCACACCAAATGACGGATGTGAGCTGCTGTTTATCATGTATGGATCGTCTCGCCTTCCACACTGCCCACCACAGGGACTCTAAATTGCCAGTGCCCTATGCACTCTGTCACCCTTTTCACTAGGGCTGCACAATAAATCGCTTCAGCATTGATATATCTATGTGCACATCTGCATTAGTAACATTGCAAGATATGCAATGTTGAGTTTGAATTATAATACCAGGAGCTACAGAATTGTATTTAATTACTGTATTTACAAGCAACTTATACTATTTCTGCAAAAAAAAAAAAAAAGTCTTGTTTCTTGTCCAAATATCTACATTTCAAAGCGAAAAACAAATATATTTTACTTGCTTCATTGGTAGATATTCGATTCAATATTTTTACTGCTCTAATTTTTTTTAATATTTGGATTAGAAACGAGACAAAGCAAAGTTTGCATTGTGATTATTTAATTTCTGTTCCTAAATATTGTTAGACATCTCAGAAAACTGTCCAATAAAGCTCTTGTGAAGCTATTTATATCGCAGTATTTATTGCAGAAAAATAAAATATCACCCATCCTTTTCAGTTTAGTAGTGACACCCTAAGCAACATCTCCTGGTACTTTGATAACTGGACCAAACAAAGTGATGTGCACCCCTGGTTATGAGCTCAACTTGATCCTTTGGCCTATTAGTATTGCTCTGCTAATGATGTGTGTGTATTATGCTGGGTCAG
Seq C2 exon
GTACGAGAGCGCTTCCTAAAAGAGCCTGCTTTTGAAGACATCACGCTGGAGTCCGAGAGGAAGAGAATATTCAAAGACTTCATGCATGTTCTAGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000058467:ENSDART00000081326:20
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.870 A=NA C2=0.188
Domain overlap (PFAM):
C1:
PF0184614=FF=PU(46.2=52.2)
A:
NA
C2:
PF0184614=FF=PD(50.0=81.2)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CTCGAGAAGGCTGAAGCACG
R:
TCTAGAACATGCATGAAGTCTTTGA
Band lengths:
230-2179
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]