RnoINT0106783 @ rn6
Intron Retention
Gene
ENSRNOG00000019746 | Paf1
Description
PAF1 homolog, Paf1/RNA polymerase II complex component [Source:RGD Symbol;Acc:1306219]
Coordinates
chr1:85366011-85366497:-
Coord C1 exon
chr1:85366405-85366497
Coord A exon
chr1:85366133-85366404
Coord C2 exon
chr1:85366011-85366132
Length
272 bp
Sequences
Splice sites
5' ss Seq
CAGGTATGA
5' ss Score
9.46
3' ss Seq
AGGTATGTTTTCCCACCCAGGTT
3' ss Score
7.33
Exon sequences
Seq C1 exon
GTCTGGAGTGGTCTGCCGAGTCAAGTACTGCAACAGCCTTCCTGACATCCCATTTGACCCCAAATTCATCACCTACCCCTTCGACCAGAACAG
Seq A exon
GTATGACCAAACTCAGTGGATAAGCTATTAAAAATAGTTCATTGAAAGCAAGGACTGCTTATTTCATTGCCTCTTCCTGCCTATGATTGGCACATAGGAAGTGCTCAGTAACTACTAATAGAGAAAGCAGCATGCAAAACCCTTCTTACTCAGAAGCTGCCAATACTGGACACTTACACTCCCTCTCCATAGAAGCTTAACATCTAGGAAGGAAGCATGTTGGGATGTGAGGGTGGATCATAAAGCTATAACAGGTATGTTTTCCCACCCAG
Seq C2 exon
GTTTGTTCAGTACAAAGCAACCTCCTTGGAGAAACAGCATAAACATGACCTCCTGACTGAACCAGATCTGGGGGTCACCATCGATCTCATCAACCCTGACACCTACCGCATTGATCCCAATG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000019746:ENSRNOT00000026778:3
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=0.119
Domain overlap (PFAM):
C1:
PF039858=Paf1=PU(7.1=93.8)
A:
NA
C2:
PF039858=Paf1=FE(13.4=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TCTGGAGTGGTCTGCCGAG
R:
TTGGGATCAATGCGGTAGGTG
Band lengths:
212-484
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]