BtaINT0158383 @ bosTau6
Intron Retention
Gene
ENSBTAG00000020311 | USP20
Description
Bos taurus ubiquitin specific peptidase 20 (USP20), mRNA. [Source:RefSeq mRNA;Acc:NM_001105333]
Coordinates
chr11:100264221-100264837:+
Coord C1 exon
chr11:100264221-100264358
Coord A exon
chr11:100264359-100264727
Coord C2 exon
chr11:100264728-100264837
Length
369 bp
Sequences
Splice sites
5' ss Seq
AAGGTTCGG
5' ss Score
5.96
3' ss Seq
CCAGGATGTGGTGCCCCCAGCCC
3' ss Score
3.11
Exon sequences
Seq C1 exon
AGCCGGACAACGAGGCGCACATGCGCAGCTCCCGGCCCTGCAGCCCCGTCCACCACCACGAAGGCCACGCCAAGCTGGCCAGCAGCCCTCATCGTGCGAGCCCTGTGAGGATGGGGCCGGCCTATGTGCTCAAGAAAG
Seq A exon
GTTCGGAGGAGCGGGCAGGTGGAGAGGGGAGGCGGGCAGGGCCTCCCATCCTGGAGCTCGGGCAGGGGGCGGGAGCGGGGCGGGTGGCGGAGGTTGCACCCCTGGTGGTGATGTTTGGTTCGCGAGCACTTGCTACCAGGGGCTGTGCCAGGCGCCCTTCACGCGGTGTCTCTGAGCCGTCCTAACATGGCTGGGACACGAGTTGTTGCTGGGGGGGCTCCCACAGACCCAGGAGGTGGAGTGGGAGCTGGTCACGTGACTCGTACAGGCGTGACCACCCAGCGCCTGCCCCTGGCGCCGGGCAGGCGGGCGGGGCGGGGCGGGGCGGGGCCTAGTCCCAGGTCTAGCCCCAGGATGTGGTGCCCCCAG
Seq C2 exon
CCCAGGTCCCCGGCAGCCGGCGGCGGAAGGAGCAGAGCTACCGCAGCGTCATCTCGGACATCTTCGACGGCTCCGTCCTCAGCCTCGTGCAGTGTCTCACCTGTGACCGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000020311:ENSBTAT00000027070:12
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=1.000 A=NA C2=0.189
Domain overlap (PFAM):
C1:
PF0044324=UCH=FE(8.6=100)
A:
NA
C2:
PF0044324=UCH=FE(6.7=100)
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:
GGACAACGAGGCGCACATG
R:
GTCACAGGTGAGACACTGCAC
Band lengths:
241-610
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development