RnoINT0118352 @ rn6
Intron Retention
Gene
ENSRNOG00000052539 | Prpf40b
Description
pre-mRNA processing factor 40 homolog B [Source:RGD Symbol;Acc:1565411]
Coordinates
chr7:140979968-140980404:+
Coord C1 exon
chr7:140979968-140980054
Coord A exon
chr7:140980055-140980226
Coord C2 exon
chr7:140980227-140980404
Length
172 bp
Sequences
Splice sites
5' ss Seq
TCAGTGAGT
5' ss Score
7.68
3' ss Seq
GTATCTACTCATCTGCCCAGGGC
3' ss Score
5.64
Exon sequences
Seq C1 exon
ACTGAATGCCAGCACCTCCACACCAAAGGCCGAAAGCATGGCAGAAAGGGCAGGAAACACCATCGCAAGCGTTCGCACACCCCCTCA
Seq A exon
GTGAGTCGGCAGGTAGAGGGACATGGGTGAGGCGGGACTGTTTCATACAAATTAAACACATCTTTCCCTATACATTACCTCCTTGGCTCTGGACTCCCTGTCCCCAGTTCCCAGATGAGGGCTTCTGGAAGACAGAACCTCTGGGCTGACCGGTATCTACTCATCTGCCCAG
Seq C2 exon
GGCTCTGAGTCAGATGAAGAGGAGCTGCCCCCACCATCCCTCCGGCCCCCCAAGCGGAGGCGGCGGAACCCTTCAGAATCTGGCTCTGAGCCTTCCTCCTCACTTGATTCAGTTGAAAGTGGGGGTGCTGCCCTTGGAGGACCAGGCTCCCCATCTTCCCACCTTCTTCTTGGGTCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000052539:ENSRNOT00000091306:21
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.931 A=NA C2=1.000
Domain overlap (PFAM):
C1:
NO
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:
CAGCACCTCCACACCAAAGG
R:
AGAAGGTGGGAAGATGGGGAG
Band lengths:
245-417
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]