RnoINT0118353 @ rn6
Intron Retention
Gene
ENSRNOG00000052539 | Prpf40b
Description
pre-mRNA processing factor 40 homolog B [Source:RGD Symbol;Acc:1565411]
Coordinates
chr7:140980227-140980716:+
Coord C1 exon
chr7:140980227-140980404
Coord A exon
chr7:140980405-140980654
Coord C2 exon
chr7:140980655-140980716
Length
250 bp
Sequences
Splice sites
5' ss Seq
CAGGTAAGC
5' ss Score
9.88
3' ss Seq
TGTTTTTTGTAAACCTGTAGATC
3' ss Score
7.81
Exon sequences
Seq C1 exon
GGCTCTGAGTCAGATGAAGAGGAGCTGCCCCCACCATCCCTCCGGCCCCCCAAGCGGAGGCGGCGGAACCCTTCAGAATCTGGCTCTGAGCCTTCCTCCTCACTTGATTCAGTTGAAAGTGGGGGTGCTGCCCTTGGAGGACCAGGCTCCCCATCTTCCCACCTTCTTCTTGGGTCAG
Seq A exon
GTAAGCAGTTTCTAGGAGCCTGGGAGCTGGAGTAGAGACCCCTGAGGCTTGTCCGGGATTGGGAGGGTCTCGCTGTGTAGCAAGACTTCCTGTCCCTGCCCAGGCAAGGATCTAGGTGAAGGAAGGAAAGCCAGACTCGGCCTTCCTCAGACCACATCTACAAAGAATGTACAGGCAGAGGGTGAGCCTTCTTTTCCTCCCAGCGGGGCTCAGCATGGAGGTTTGTTTTTTGTTTTTTGTAAACCTGTAG
Seq C2 exon
ATCATGGTCTTCGGAAAACCAAGAAACCAAAAAAGAAAACTAAGAAAAGAAGACACAAGTCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000052539:ENSRNOT00000091306:22
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=1.000 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:
GGCTCTGAGTCAGATGAAGAGG
R:
CGACTTGTGTCTTCTTTTCTTAGT
Band lengths:
240-490
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]