RnoINT0118318 @ rn6
Intron Retention
Gene
ENSRNOG00000004864 | Prpf40a
Description
pre-mRNA processing factor 40 homolog A [Source:RGD Symbol;Acc:1311401]
Coordinates
chr3:38697421-38697988:-
Coord C1 exon
chr3:38697924-38697988
Coord A exon
chr3:38697586-38697923
Coord C2 exon
chr3:38697421-38697585
Length
338 bp
Sequences
Splice sites
5' ss Seq
CAGGTAATA
5' ss Score
8.55
3' ss Seq
ATTATTTTATTATTTTGTAGTGC
3' ss Score
6.66
Exon sequences
Seq C1 exon
CGGGTACCCTCCAATGCTTCATGGGAGCAAGCTATGAAAATGATCATAAATGATCCTCGGTACAG
Seq A exon
GTAATACAACAATTTATACATTTTCTTTTTACGTTAATCTTAGGGCATTTAAAATTGTGTCCAACAGTCTAACTGCATAAAGAGTTGTTGTTCATAGCTTTGTAGTTGGCATAGAGGTATTCTATGCATGCTACAGCCAAAACCCCAAAGACTTGTCCTGCAGTCTGAGCACCATAGAATCATTTTAAAACTAGAAGTTGCATTTTAGAATCATTTTATATCTTCAATAAATTACACAAATGTTTTTAATATATGCATGAAACTTTTTTCCAAAGCATTAACATTTGTTTCTCCAGCCTTTATGCTTAATCCTATATGATTATTTTATTATTTTGTAG
Seq C2 exon
TGCTTTAGCAAAGCTGAGTGAGAAGAAGCAGGCATTTAATGCCTATAAAGTCCAGACAGAGAAGGAGGAAAAAGAAGAAGCAAGATCAAAATACAAAGAAGCTAAGGAATCCTTTCAGCGTTTTCTTGAAAATCATGAAAAAATGACTTCCACAACCAGATACAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000004864:ENSRNOT00000006549:12
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.227 A=NA C2=0.357
Domain overlap (PFAM):
C1:
PF0184614=FF=FE(42.0=100)
A:
NA
C2:
PF0184614=FF=PD(30.0=26.8),PF0184614=FF=PU(44.0=39.3)
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:
ACCCTCCAATGCTTCATGGGA
R:
TTGTATCTGGTTGTGGAAGTCA
Band lengths:
225-563
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]