RnoINT0118341 @ rn6
Intron Retention
Gene
ENSRNOG00000052539 | Prpf40b
Description
pre-mRNA processing factor 40 homolog B [Source:RGD Symbol;Acc:1565411]
Coordinates
chr7:140971012-140971721:+
Coord C1 exon
chr7:140971012-140971076
Coord A exon
chr7:140971077-140971556
Coord C2 exon
chr7:140971557-140971721
Length
480 bp
Sequences
Splice sites
5' ss Seq
CAGGTACGC
5' ss Score
10.12
3' ss Seq
TCCTCAACTGTCCACTCCAGTGC
3' ss Score
5.99
Exon sequences
Seq C1 exon
GCTGTCCCTTCCAATGCTTCCTGGGAACAGGCCATGAAGATGGTAGTCACTGACCCACGTTACAG
Seq A exon
GTACGCCTGAGGAGGAGTGGATAGTCCTTGTTGGTGAAAGCAAATGGGCTAGGAACTCCCTGAGATGTCCCAATTTGAATTGATACTCAACGGAGTTGACTCCCAATTGGGTGCTGACACTCAGGTCTAAGTGGCTGAGATGGGGTGCAAGAGAAAGAAAAGCTAGAGTAGCTCCAGGATGCACAGAGGGAAATCGTACAGCCATGAGATGGTTAGTAAATGATTACTGGCTTGAATTAAAATTAGGGAAATAGGGGCTCTAAGGAGACATGTCTGACGGTAACTTGAAGCAGAAGGGTCCAGTATTTCTTCCCCTCACTCCTCATCCTACCCATATTCTGGACACCTGTATGCTAAGTCTATGCACGAGGCTCCACTTTGGTGCTGTGGAGACCTTTCCCCCAAGTCTGAGATCCTGCTTCATGGGCCGCCAGGGTCATTCATGCTGCATCCCCTCCTTTCCTCAACTGTCCACTCCAG
Seq C2 exon
TGCCTTGCCCAAACTGAGTGAGAAGAAGCAGGCGTTTAATGCTTATAAGGCTCAGCGGGAGAAAGAGGAGAAAGAGGAGGCCCGGCTGAGAGCCAAGGAGGCCAAGCAGACTCTGCAGCATTTCCTGGAGCAGCATGAACGCATGACCTCCACCACCCGCTACCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000052539:ENSRNOT00000091306:11
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.773 A=NA C2=0.821
Domain overlap (PFAM):
C1:
PF0394210=DTW=FE(17.6=100),PF0184614=FF=FE(42.0=100)
A:
NA
C2:
PF0394210=DTW=FE(46.2=100),PF0184614=FF=PD(30.0=26.8)
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:
GCTGTCCCTTCCAATGCTTCC
R:
CGGTAGCGGGTGGTGGAG
Band lengths:
230-710
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]