RnoINT0118340 @ rn6
Intron Retention
Gene
ENSRNOG00000052539 | Prpf40b
Description
pre-mRNA processing factor 40 homolog B [Source:RGD Symbol;Acc:1565411]
Coordinates
chr7:140970802-140971076:+
Coord C1 exon
chr7:140970802-140970928
Coord A exon
chr7:140970929-140971011
Coord C2 exon
chr7:140971012-140971076
Length
83 bp
Sequences
Splice sites
5' ss Seq
AAGGTGCTG
5' ss Score
4.05
3' ss Seq
CCTATGCCTCTCTGTTCCAGGCT
3' ss Score
9.69
Exon sequences
Seq C1 exon
TTCTACTGGACAGCATCGGCTACCACAGGAAGAGGAGGAAGCTAAGCCAGAACCAGAGAGATCGGGCCTCAGTTGGAGCAACCGGGAGAAGGCAAAGCAGGCATTCAAAGAGCTGCTAAGGGACAAG
Seq A exon
GTGCTGGGGATTTGAAAGGTTAAGGGAAGGCCTGGAGGGCTTGAATGTTACCAGGCTCCAAGACCTATGCCTCTCTGTTCCAG
Seq C2 exon
GCTGTCCCTTCCAATGCTTCCTGGGAACAGGCCATGAAGATGGTAGTCACTGACCCACGTTACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000052539:ENSRNOT00000091306:10
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=1.000 A=NA C2=0.773
Domain overlap (PFAM):
C1:
PF0394210=DTW=PU(30.3=83.7),PF0184614=FF=PU(24.0=27.9)
A:
NA
C2:
PF0394210=DTW=FE(17.6=100),PF0184614=FF=FE(42.0=100)
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:
ATCGGCTACCACAGGAAGAGG
R:
AACGTGGGTCAGTGACTACCA
Band lengths:
174-257
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]