RnoINT0118323 @ rn6
Intron Retention
Gene
ENSRNOG00000004864 | Prpf40a
Description
pre-mRNA processing factor 40 homolog A [Source:RGD Symbol;Acc:1311401]
Coordinates
chr3:38689895-38690280:-
Coord C1 exon
chr3:38690166-38690280
Coord A exon
chr3:38689987-38690165
Coord C2 exon
chr3:38689895-38689986
Length
179 bp
Sequences
Splice sites
5' ss Seq
CTGGTGAGA
5' ss Score
7.54
3' ss Seq
TTCTTTAGTTTTTTCATTAGGAT
3' ss Score
6.29
Exon sequences
Seq C1 exon
ATCTTTCTAGACGAGTTGCATGAGCACGGGCAGCTGCACTCTATGTCCTCTTGGATGGAGCTGTATCCGACCATTAGCTCTGACATTCGATTCACTAATATGCTGGGTCAGCCTG
Seq A exon
GTGAGACGCTTTTGTTTCCACACATACTGTAGGAGTTGGGATGGATGTGGGGGGGGGGGCGTGGGACCAGTTGATGGGAAGGAGGGGTGTGTGCTTTATTTTATGTTTGTTTTACAAACAAAAGTAATTGCAGCTCTTGGTTAGAGCTAGCTTTTTGACTTCTTTAGTTTTTTCATTAG
Seq C2 exon
GATCAACTGCACTTGATCTTTTCAAGTTTTATGTTGAAGATCTTAAAGCACGATATCATGATGAAAAAAAGATAATAAAAGACATTCTGAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000004864:ENSRNOT00000006549:17
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=0.000
Domain overlap (PFAM):
C1:
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:
TCTTTCTAGACGAGTTGCATGAGC
R:
TCATCATGATATCGTGCTTTAAGATC
Band lengths:
178-357
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]