RnoINT0118359 @ rn6
Intron Retention
Gene
ENSRNOG00000052539 | Prpf40b
Description
pre-mRNA processing factor 40 homolog B [Source:RGD Symbol;Acc:1565411]
Coordinates
chr7:140969562-140970097:+
Coord C1 exon
chr7:140969562-140969672
Coord A exon
chr7:140969673-140969976
Coord C2 exon
chr7:140969977-140970097
Length
304 bp
Sequences
Splice sites
5' ss Seq
GAGGTCCTG
5' ss Score
-2.13
3' ss Seq
TTTGACCCATTCCCTTACAGCTG
3' ss Score
10.56
Exon sequences
Seq C1 exon
AGGGCCTTATGGAGTGAACACGTGGCCCCTGACGGGCGCATCTACTACTACAATGCAGATGATAAGCAATCCGTGTGGGAGAAGCCCAGCGCACTCAAGTCTAAAGCCGAG
Seq A exon
GTCCTGAGTGGGCTTTTCTGGTTCTTCCTTTCAGTTTCCCTGGTCCTTTCAAGTTCTCAGCCTTCCTTGAGTCTCCAACCATTCTCATTGTGGTTCCTCTGACCCCAAGCCCCTGACCACCTCCATGCTCCTTGTGATTGCCTCCCTAGGAGCAATCTCAGGAGGTCCACTCCCCCTTCAGGCCAGGCCAGGTGACAACGAAAGCCTGCTGTCTTTCCTATCTTCTACTCACTGCGTCCCCTTCACCCCCTGACAGGCTGGAGAGCTTTCCAGCTGCTGATGACTTTGACCCATTCCCTTACAG
Seq C2 exon
CTGCTACTGTCCCAGTGTCCCTGGAAAGAGTATAAATCAGACACAGGAAAGCCTTACTACTACAACAACCAGAGTCAGGAGTCCCGTTGGACCCGACCCAAGGACCTGGATGACCTGGAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000052539:ENSRNOT00000091306:6
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.432 A=NA C2=0.659
Domain overlap (PFAM):
C1:
PF0039721=WW=PD(90.3=75.7)
A:
NA
C2:
PF0039721=WW=WD(100=73.2)
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:
GGGCCTTATGGAGTGAACACG
R:
CTTCCAGGTCATCCAGGTCCT
Band lengths:
231-535
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]