RnoINT0118351 @ rn6
Intron Retention
Gene
ENSRNOG00000052539 | Prpf40b
Description
pre-mRNA processing factor 40 homolog B [Source:RGD Symbol;Acc:1565411]
Coordinates
chr7:140979693-140980054:+
Coord C1 exon
chr7:140979693-140979788
Coord A exon
chr7:140979789-140979967
Coord C2 exon
chr7:140979968-140980054
Length
179 bp
Sequences
Splice sites
5' ss Seq
GAGGTAAGA
5' ss Score
10.06
3' ss Seq
TCTCCCTCTGCCTCTAGCAGACT
3' ss Score
7.01
Exon sequences
Seq C1 exon
GTCCGTGAGCGCTTTGTGTGCGACTCAGCCTTTGAGCAGATCACCCTGGAGTCGGAGCGGATCCGGCTCTTTCGAGAGTTCCTGCAGGTGCTGGAG
Seq A exon
GTAAGATACTTGGCCACCCTCATCTATGTACCTTGGAACTCCTAGGCCTGCATGAGACCTTCAGTAGCTTGTCACCATGAAGGCCCTTTTACCTGCCCAGCCAAGGAAGGGGAGGGCTGAGGGTGCCCTAGAATAGACAGAAAGCAAGGTTCTTTTACCTCTCCCTCTGCCTCTAGCAG
Seq C2 exon
ACTGAATGCCAGCACCTCCACACCAAAGGCCGAAAGCATGGCAGAAAGGGCAGGAAACACCATCGCAAGCGTTCGCACACCCCCTCA
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000052539:ENSRNOT00000091306:20
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=0.931
Domain overlap (PFAM):
C1:
PF0184614=FF=PD(50.0=81.2)
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TCCGTGAGCGCTTTGTGTG
R:
GGGGTGTGCGAACGCTTG
Band lengths:
178-357
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]