DreINT0109692 @ danRer10
Intron Retention
Gene
ENSDARG00000098432 | paf1
Description
paf1, RNA polymerase II associated factor, homolog (S. cerevisiae) [Source:ZFIN;Acc:ZDB-GENE-050506-101]
Coordinates
chr15:46790359-46790629:-
Coord C1 exon
chr15:46790524-46790629
Coord A exon
chr15:46790428-46790523
Coord C2 exon
chr15:46790359-46790427
Length
96 bp
Sequences
Splice sites
5' ss Seq
TCAGTGAGG
5' ss Score
2.91
3' ss Seq
TCTCTGTTGGATTCTTTCAGATT
3' ss Score
8.87
Exon sequences
Seq C1 exon
GATCGGTGTGTCCGTCAAGCAGCAGTTCACAGAGGAGGAGATCTATAAAGACAGAGACAGTCAGATCGCTGCCATTGAGAAGACCTTCGAAGACGCTCAGAAATCA
Seq A exon
GTGAGGGAACAAACACACTCACACACACACACACACACACACACACACACACACACACACTGATTTCTAAGCTCACTCTCTGTTGGATTCTTTCAG
Seq C2 exon
ATTTCCCAGCATTACAGCAAACCCAGAGTCACACCGGTGGAGGTGCTGCCCGTCTTCCCTGACTTCAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000098432:ENSDART00000168722:3
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=0.000
Domain overlap (PFAM):
C1:
PF039858=Paf1=FE(10.0=100)
A:
NA
C2:
PF039858=Paf1=FE(6.3=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:
GTGTCCGTCAAGCAGCAGTTC
R:
CTTGAAGTCAGGGAAGACGGG
Band lengths:
168-264
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]