RnoINT0118345 @ rn6
Intron Retention
Gene
ENSRNOG00000052539 | Prpf40b
Description
pre-mRNA processing factor 40 homolog B [Source:RGD Symbol;Acc:1565411]
Coordinates
chr7:140973083-140973824:+
Coord C1 exon
chr7:140973083-140973216
Coord A exon
chr7:140973217-140973709
Coord C2 exon
chr7:140973710-140973824
Length
493 bp
Sequences
Splice sites
5' ss Seq
CAGGTATTT
5' ss Score
7.51
3' ss Seq
TCTGGCTTTTCCCTGTTCAGACC
3' ss Score
9.59
Exon sequences
Seq C1 exon
ACATGGACAAAGAAGATGCACTCATCTGCTTTGAGGAGCACATCCGAGCTTTGGAGAGAGAGGAGGAGGAAGAGCGGGAACGCGCCCGGCTTCGGGAACGGCGCCAGCAGCGGAAGAATCGGGAGGCTTTTCAG
Seq A exon
GTATTTTCATACCCTTCATGATCAGAGCTCAGCTCAGCTCAGCTCTAGACCACAGCCTCTTTGCAGTGACCCGTCTCTGAACGAGGCTGTCTGTTGACTGGCCCCTTTCAAGTTCCGCAAGGCCACTCTATAGTAGTGCTCCTTCAGGGAGCTAGGCTGTATGTACACCCTCAGTCATGAGTGCCAGCTAGACCAAGTGTCTTCCTTCCAAGTGTCTTGAGAGCCAGACAGTTTTTCCTCAGCTCAGCAGTGGTAGTAGTGGGCTGGCTAAGTTGGTCATAGCAGGAAATTGTGCACCCTGAGGTCTCGGATTCATTGCCTTCAGGCTGGCTTATCGGTTGTATACTCACATTTTCTCCTGTAGTGCCTTTGCCTACTTTGCCTGAGTTGCTTCTGCTTGTCCCTCTGCCGTTCCTTTTCACCTCCTCAGACCTGGCTGTGTTTCCCCAGCTGTCTCAGTCTCCTTTCCCTCTTCTGGCTTTTCCCTGTTCAG
Seq C2 exon
ACCTTCCTGGACGAGCTGCATGAGACAGGGCAGCTGCACTCCATGTCCACCTGGATGGAGCTGTACCCAGCAGTCAGCACCGATGTTCGCTTTGCCAACATGCTGGGCCAGCCGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000052539:ENSRNOT00000091306:15
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.333 A=NA C2=0.013
Domain overlap (PFAM):
C1:
PF0184614=FF=PD(23.2=28.9),PF091066=SelB-wing_2=PU(46.3=42.2),PF0184614=FF=PU(10.7=13.3)
A:
NA
C2:
PF091066=SelB-wing_2=PD(48.8=51.3),PF0184614=FF=FE(67.9=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:
ACATGGACAAAGAAGATGCACTCA
R:
CAGCATGTTGGCAAAGCGAAC
Band lengths:
239-732
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]