RnoINT0118348 @ rn6
Intron Retention
Gene
ENSRNOG00000052539 | Prpf40b
Description
pre-mRNA processing factor 40 homolog B [Source:RGD Symbol;Acc:1565411]
Coordinates
chr7:140979081-140979482:+
Coord C1 exon
chr7:140979081-140979197
Coord A exon
chr7:140979198-140979344
Coord C2 exon
chr7:140979345-140979482
Length
147 bp
Sequences
Splice sites
5' ss Seq
AGTGTGAGG
5' ss Score
2.87
3' ss Seq
CTGTTTCTTTTTGCCTTCAGCTG
3' ss Score
10.25
Exon sequences
Seq C1 exon
GACCGGGGCTTCTGTGTGGAGGTGAACACAGCCTTTGAGGACTTCGCCCACGTCATAAGCTTTGACAAGAGGGCTGCTGCGCTGGACGCAGGCAACATCAAGCTGACCTTCAACAGT
Seq A exon
GTGAGGGGACGGGCAGGGCTGGGTGGGCCTCTCTCTTACCTCAGTGTCTTGTTCCTAACTGCCCTGCTGGTTATCTTGGGATTTAGACCTGCCTTCCTGCCTCTCTTGAGGTACTCCTGACCCTGCTCTGTTTCTTTTTGCCTTCAG
Seq C2 exon
CTGCTGGAAAAAGCAGAGGCACGGGAGAGGGAACGGGAAAAGGAGGAGGCCCGAAGGATGCGGCGCAGAGAAGCTGCCTTTCGAAGCATGCTGAGGCAGGCCGTGCCTGCTCTGGAGCTGGGCACTGCCTGGGAAGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000052539:ENSRNOT00000091306:18
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.304
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0184614=FF=PU(46.2=52.2)
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:
CGGGGCTTCTGTGTGGAGG
R:
GCAGTGCCCAGCTCCAGAG
Band lengths:
242-389
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]