RnoINT0118320 @ rn6
Intron Retention
Gene
ENSRNOG00000004864 | Prpf40a
Description
pre-mRNA processing factor 40 homolog A [Source:RGD Symbol;Acc:1311401]
Coordinates
chr3:38696151-38697007:-
Coord C1 exon
chr3:38696899-38697007
Coord A exon
chr3:38696302-38696898
Coord C2 exon
chr3:38696151-38696301
Length
597 bp
Sequences
Splice sites
5' ss Seq
AAGGTACTC
5' ss Score
7.46
3' ss Seq
TATTCAAACATTTGTTGTAGGAA
3' ss Score
6.63
Exon sequences
Seq C1 exon
AAAAGCTGAGCAAATGTTTGGGGAGATGGAAGTTTGGAATGCAATATCAGAGCGTGATCGTCTTGAAATCTATGAAGACGTTTTGTTCTTCCTTTCAAAGAAAGAAAAG
Seq A exon
GTACTCTTAAAATCATAAGTATTTTCAACATTTTTAAGGATTTTACTTTAAAAGAATAAAACTATAACAGAATTTCTTGACTTAATTTGTATAGTGTATGTTATATATCATATCTGCTCATTGGAAGCTATGTTCAAGATAAAATGAGTTAACTCAATCTTTTTCCCTCTTTTCGAAGATGGTAATTATTGTTTAAATCATAGTGGGTGCTGATTTATCTGAATATTTATCACTGTTAAATTGTTTTACATCCATTTTTAAAGGATATTACTAAAACTTTAAATAGAATTGAATGACATTGAGGACTTTGGTATTTACATGCTATGACTGCTTTCAGTAGCCCTCATTGTAAAATGTATCTGTACTGCATATTGGTAATACAGACACAAAAACAAAGTTTTGGATTTTGACTTCAAAGACAGATGGAAAAAGTAAAAGTAAGGACTCTGTCACAAACAACAGTAACAAAATAAACAGTGTTGATACTGCAGAACTATATAAAACATTTGAAGCTTATCAGAATATAAAATAATGTTAAGTAATTGCAATTCAGATATCTTGTTTGAATGTTAAAAGGTATTCAAACATTTGTTGTAG
Seq C2 exon
GAACAAGCAAAGCAGTTACGAAAGAGAAATTGGGAAGCCTTAAAAAACATACTTGACAATATGGCTAATGTTACATACTCTACCACTTGGTCTGAAGCCCAGCAGTATCTGATGGATAATCCAACGTTCGCAGAGGATGAAGAGTTACAGA
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000004864:ENSRNOT00000006549:14
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.027 A=NA C2=0.196
Domain overlap (PFAM):
C1:
PF0184614=FF=PD(54.0=73.0)
A:
NA
C2:
PF0184614=FF=PU(75.0=82.4)
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:
AAAGCTGAGCAAATGTTTGGGG
R:
AACTCTTCATCCTCTGCGAACG
Band lengths:
254-851
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]