RnoINT0118349 @ rn6
Intron Retention
Gene
ENSRNOG00000052539 | Prpf40b
Description
pre-mRNA processing factor 40 homolog B [Source:RGD Symbol;Acc:1565411]
Coordinates
chr7:140979345-140979788:+
Coord C1 exon
chr7:140979345-140979482
Coord A exon
chr7:140979483-140979692
Coord C2 exon
chr7:140979693-140979788
Length
210 bp
Sequences
Splice sites
5' ss Seq
GAGGTCAGA
5' ss Score
5.24
3' ss Seq
CAGTGCTCTCCCCGTTCAAGGTC
3' ss Score
6.9
Exon sequences
Seq C1 exon
CTGCTGGAAAAAGCAGAGGCACGGGAGAGGGAACGGGAAAAGGAGGAGGCCCGAAGGATGCGGCGCAGAGAAGCTGCCTTTCGAAGCATGCTGAGGCAGGCCGTGCCTGCTCTGGAGCTGGGCACTGCCTGGGAAGAG
Seq A exon
GTCAGAAGCACAGCCTGGCCCCAATCACCCTCAGGCCTGAGGGCAGCGAAGCTTCTCCACCACTGAGGGCCCACCCCAGTCACAGCACAAGCCCTGGGCCAGCTCCAGTTCCCTTCCTTCCTCTGCCCCAGCCCTGCCCAGTTCTCGTGGCGGTGTCCAAGCTGGTCCAGGCAGGCCCTGGTCTGATCAGCAGTGCTCTCCCCGTTCAAG
Seq C2 exon
GTCCGTGAGCGCTTTGTGTGCGACTCAGCCTTTGAGCAGATCACCCTGGAGTCGGAGCGGATCCGGCTCTTTCGAGAGTTCCTGCAGGTGCTGGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000052539:ENSRNOT00000091306:19
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.304 A=NA C2=0.000
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:
CTGGAAAAAGCAGAGGCACGG
R:
CAGCACCTGCAGGAACTCTC
Band lengths:
228-438
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]