RnoINT0118327 @ rn6
Intron Retention
Gene
ENSRNOG00000004864 | Prpf40a
Description
pre-mRNA processing factor 40 homolog A [Source:RGD Symbol;Acc:1311401]
Coordinates
chr3:38688798-38689434:-
Coord C1 exon
chr3:38689297-38689434
Coord A exon
chr3:38688894-38689296
Coord C2 exon
chr3:38688798-38688893
Length
403 bp
Sequences
Splice sites
5' ss Seq
GATGTAGGT
5' ss Score
4.9
3' ss Seq
TCCATATCATTGCTTTCCAGATC
3' ss Score
8.74
Exon sequences
Seq C1 exon
TTACTAGAAAAGGCAGAAGCCCGTGAACGTGAGAGAGAAAAGGAAGAAGCTCGGAAAATGAAACGAAAAGAGTCTGCCTTTAAGAGTATGTTGAAACAGGCCACTCCTCCAATAGAACTGGATGCTGTCTGGGAAGAT
Seq A exon
GTAGGTATATTTGTGCTTCACAGTTGAAAAGACCACTGATTTGTTTGTAGGGGACACAGATAAGCTAAATAAAACTATTTATAAAACATTGTATATATGTCAAAAGTTAGTTGTGACTTGAATTTAGAAATAGTTTGTCTAAAATGGTTTGAATACACTATTACTAGGGGACAGGGTTTCTCTTCACAGCACTGGTTGTCTTAGAACTCTGTAGGCCAGGCTACACAGATCTACCTGCCTCTGTCTCCGGGCATGTACTACCACACCCTGCTAGAACTTTTGAAGGGAGAAAAAATTTCTCTCTTCGTGAATCACAGTTTTCCCTATAGGTCATGCTTCTTTTAGACATGGTGATAAAATTTTCTTCATCTTTGTATATTTATTCCATATCATTGCTTTCCAG
Seq C2 exon
ATCCGGGAAAGATTTGTGAAGGAACCAGCATTTGAGGATATAACTCTAGAATCTGAAAGAAAAAGAATATTTAAAGATTTCATGCATGTGCTTGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000004864:ENSRNOT00000006549:20
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.449 A=NA C2=0.125
Domain overlap (PFAM):
C1:
PF0184614=FF=PU(46.2=52.2)
A:
NA
C2:
PF0184614=FF=PD(50.0=81.2)
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:
GCAGAAGCCCGTGAACGTG
R:
CTCAAGCACATGCATGAAATCT
Band lengths:
222-625
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]