BtaINT0158403 @ bosTau6
Intron Retention
Gene
ENSBTAG00000020311 | USP20
Description
Bos taurus ubiquitin specific peptidase 20 (USP20), mRNA. [Source:RefSeq mRNA;Acc:NM_001105333]
Coordinates
chr11:100260162-100261405:+
Coord C1 exon
chr11:100260162-100260275
Coord A exon
chr11:100260276-100261326
Coord C2 exon
chr11:100261327-100261405
Length
1051 bp
Sequences
Splice sites
5' ss Seq
ACGGTGAGT
5' ss Score
11.45
3' ss Seq
CGGATTTGGTCTTCCTACAGCCC
3' ss Score
7.58
Exon sequences
Seq C1 exon
CCCCCCGCTCACCCAGTTCTTCTTGGAGTGTGGAGGCCTGGTCCGCACAGACAAGAAGCCAGCCCTGTGCAAAAGTTATCAGAAGCTGGTCTCTGAGGTCTGGCACAGGAAACG
Seq A exon
GTGAGTGACCGAGTCCCCGACCTCTGGCAGGGGCATGGGGACAGGCTTTCTGTCGGGCCCCTTGATGGAGCACTTCCGGTGCCCTCAACCTCTCGCCACCACAGGCCACACTTTCCCCTGTGTCATGCTTATGGGGGCCCTTCCAGGTACAGGTCACAGCCAACTCTGGCTCGCAAACTGGGGAAACTGAGGTTCAGGGAGATTCAAGCGTCTAGCCCAAGATAACACATCTTGTGAAAGGCGCAGCAAGAACTTGAACCTGGCATTGACTGCAGCTGGCAGCGCTTCAGAGCGTGTGTGCTGCGGTCTGGAGACACACGGTGACCACTCCTAGGTCTCAGCCACATCTGTGCACATTGAACAAGGTTTCAGAAGTGGTGGCTGACACTGACCAGGGGCTTTAGCTCAGTATAAAAGGAATTTAAAGACCAGATGCTTGGGGTAGATCCAGGAAAATGTTAACATTGGGAATAAAGTGAGTGCATCGAAATATATTAAATTAAAAGCAGATTATTAAACAGCATGATGCAATACAGCTCCAACTTTAAGCCACGTTCAAGTGTTTACCTGCGTGTAATTTTGTGTCTGCATTGTCCAGGAAACGTCTGGAAATCTTCATGGTCATTATCTCTGCAGGATGCTGCTAGTGTTGATGATTCTTTGCTGTGCTTTCCTGAAATTTTGTATTTTTTTTTCCGAAATTTTCTGCTGTTGAATAATGAACATGTATGACTTTTGAAATTAGAAAGCAACAGTAAATATTTCAGAATGAGAACCATTTTAAAGGAGGCATGTCACGGGCTGGCAGGACGTGATGCCATCCTAGTCAAGAGCTGACTAGGCCTGGCTGAGCCATGACTTGATGTTTTCTTTTCCTGACCTTAGAGATGTGCAGACCTGCTGGGTCCCTGGCCGGGCCAGCACCGCCCGACATCGCGGTAAACGCCACACAGAGCCTGATCTGGCCATCATGGTTGCCCAGCTGCCCTCGCAGGCTTGAGTAGCTCAGAGCAGACCACCGCCTGTACTAACGGATTTGGTCTTCCTACAG
Seq C2 exon
CCCCAGCTATGTGGTTCCCACCAGCCTGTCCCATGGGATCAAGTTGGTCAACCCAATGTTCCGAGGCTATGCCCAGCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000020311:ENSBTAT00000027070:9
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=0.037
Domain overlap (PFAM):
C1:
PF0044324=UCH=FE(7.1=100)
A:
NA
C2:
PF0044324=UCH=FE(4.8=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:
CGCTCACCCAGTTCTTCTTGG
R:
GGCATAGCCTCGGAACATTGG
Band lengths:
182-1233
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development