RnoINT0118346 @ rn6
Intron Retention
Gene
ENSRNOG00000052539 | Prpf40b
Description
pre-mRNA processing factor 40 homolog B [Source:RGD Symbol;Acc:1565411]
Coordinates
chr7:140973710-140974063:+
Coord C1 exon
chr7:140973710-140973824
Coord A exon
chr7:140973825-140973971
Coord C2 exon
chr7:140973972-140974063
Length
147 bp
Sequences
Splice sites
5' ss Seq
CGGGTAAGG
5' ss Score
10.17
3' ss Seq
CCATCTCTCCCTTTCTGTAGGCT
3' ss Score
10.62
Exon sequences
Seq C1 exon
ACCTTCCTGGACGAGCTGCATGAGACAGGGCAGCTGCACTCCATGTCCACCTGGATGGAGCTGTACCCAGCAGTCAGCACCGATGTTCGCTTTGCCAACATGCTGGGCCAGCCGG
Seq A exon
GTAAGGCAGCCAGGCTTCCCCTTGTCTGGTCTCTGGCTTCCTACCCTGCCAGCCTCTTTGGACCCAACTCCCTGGTCCTGTCCTTGACCCTACCCTGAGCCTTGGGAAGCTGCCGCCCGCCAGGCCCCCATCTCTCCCTTTCTGTAG
Seq C2 exon
GCTCGACTCCTCTGGACTTGTTCAAGTTCTATGTGGAGGAGTTGAAGGCTCGGTTCCACGATGAGAAGAAAATCATAAAGGATATTCTTAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000052539:ENSRNOT00000091306:16
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.013 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF091066=SelB-wing_2=PD(48.8=51.3),PF0184614=FF=FE(67.9=100)
A:
NA
C2:
PF0184614=FF=PD(17.9=32.3)
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:
CTTCCTGGACGAGCTGCATG
R:
CCTTTATGATTTTCTTCTCATCGTGG
Band lengths:
194-341
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]