RnoINT0106787 @ rn6
Intron Retention
Gene
ENSRNOG00000019746 | Paf1
Description
PAF1 homolog, Paf1/RNA polymerase II complex component [Source:RGD Symbol;Acc:1306219]
Coordinates
chr1:85365356-85365604:-
Coord C1 exon
chr1:85365499-85365604
Coord A exon
chr1:85365425-85365498
Coord C2 exon
chr1:85365356-85365424
Length
74 bp
Sequences
Splice sites
5' ss Seq
TCGGTAATT
5' ss Score
7.06
3' ss Seq
CACCCTTTTTCTTCTATCAGATC
3' ss Score
10.43
Exon sequences
Seq C1 exon
GATTGGGGTTTCTGTGAAACAGCAGTTCACAGAGGAAGAAATATACAAAGACAGGGACAGCCAGATCACAGCCATTGAGAAGACTTTTGAAGATGCCCAGAAATCG
Seq A exon
GTAATTGGGGGACTAGAATAGAGGCAGAAGTATGGCTCAGGTTCTTCCTCTTCTCACCCTTTTTCTTCTATCAG
Seq C2 exon
ATCTCCCAGCATTACAGCAAGCCCCGAGTGACACCAGTGGAGGTCATGCCTGTCTTCCCAGACTTTAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000019746:ENSRNOT00000026778:7
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.194 A=NA C2=0.217
Domain overlap (PFAM):
C1:
PF039858=Paf1=FE(11.5=100)
A:
NA
C2:
PF039858=Paf1=FE(5.2=100)
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:
TTTCTGTGAAACAGCAGTTCACA
R:
CTTAAAGTCTGGGAAGACAGGCA
Band lengths:
167-241
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]