RnoINT0118360 @ rn6
Intron Retention
Gene
ENSRNOG00000052539 | Prpf40b
Description
pre-mRNA processing factor 40 homolog B [Source:RGD Symbol;Acc:1565411]
Coordinates
chr7:140969977-140970212:+
Coord C1 exon
chr7:140969977-140970097
Coord A exon
chr7:140970098-140970187
Coord C2 exon
chr7:140970188-140970212
Length
90 bp
Sequences
Splice sites
5' ss Seq
AAGGTGAGG
5' ss Score
9.16
3' ss Seq
GCTCTCTTTTCCTCTTGCAGCCC
3' ss Score
11.71
Exon sequences
Seq C1 exon
CTGCTACTGTCCCAGTGTCCCTGGAAAGAGTATAAATCAGACACAGGAAAGCCTTACTACTACAACAACCAGAGTCAGGAGTCCCGTTGGACCCGACCCAAGGACCTGGATGACCTGGAAG
Seq A exon
GTGAGGTGTCCTGGAGGTAGAGGGAGGAGATCGGGCAAGACTACTGGGAGTTCTTTGCTACCCCGTGACTGCTCTCTTTTCCTCTTGCAG
Seq C2 exon
CCCTAGTCAAACAAGAGTCTGCAGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000052539:ENSRNOT00000091306:7
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.659 A=NA C2=1.000
Domain overlap (PFAM):
C1:
PF0039721=WW=WD(100=73.2)
A:
NA
C2:
NO
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:
CTGCTACTGTCCCAGTGTCCC
R:
TGCAGACTCTTGTTTGACTAGGG
Band lengths:
144-234
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]