BtaINT0158402 @ bosTau6
Intron Retention
Gene
ENSBTAG00000020311 | USP20
Description
Bos taurus ubiquitin specific peptidase 20 (USP20), mRNA. [Source:RefSeq mRNA;Acc:NM_001105333]
Coordinates
chr11:100259017-100260275:+
Coord C1 exon
chr11:100259017-100259086
Coord A exon
chr11:100259087-100260161
Coord C2 exon
chr11:100260162-100260275
Length
1075 bp
Sequences
Splice sites
5' ss Seq
CTGGTAGGT
5' ss Score
8.37
3' ss Seq
CTCCCTGCCCCCTCCCCCAGCCC
3' ss Score
9.97
Exon sequences
Seq C1 exon
GCCTCACGGGCATGAAGAACCTCGGCAACTCCTGCTACATGAATGCGGCCTTGCAGGCTCTGTCCAACTG
Seq A exon
GTAGGTTTCGCCTCATCTGGGATTTGGGGGGCCCTGGGAATAGCAGCTGCCGCCCCCAAGTTGGGGCGTGTGTGTTGCTCATAGAAGCCTGGATGTGGGTACACATCAAAACGCCCCAAGCCACACCTGCCCTTTGACCCAGCAATCCCTCCAATGGGAATTTCTCCTAAAGGAGGTACCAGTACCCAGAGAGGTTGAAAAAGCTGTCTGTGCTGTTCCTCACCCTGCCATTTATTGGAAACATGTTAAAGGCCCATAAAAATCACAAATTCAGTACAGACCAGCTTTACGGTGAGTTCAGGGAAAAATGGTGCAGGACAATATTTACTGAAACGGGGAGGAGTTCAGAATATGATAAGTAGGAAAAGGTTGTGATCCTTTATATGGTGCAGTCCCATTTTAGGGGTGAAAATATTTTTTTCCATCTAAGACACCCTCTACTCCCTGAGGCTGGGCCATCTCCTCTGCCTGGCACTCAGGGTCTCACACCTACTAAGGGTTCTGTGTGTGTGTGTGTGTGTGTGTGTGAGAGAGAGAGAGAAGGAGGGCAAGGATGGGGGCTCTGCATGCATAGAAAATTCTAGGAGGATATCTTCAGAGTAGCTATCCCCACTCATGGTAGGATTAAGGTCAGTTACTATTGTTTGCTTATCTGTATTTCCTAATTTTTCTACAATAAATGACTATTTCTTATGTAACGAGGTAACAAAAACAAAGAAAAAAGAAGCGAGGGAGAGGCCTTCAGGTTCAGGAAGGTTTCTAAGCAGGGGCCGATGAAAGGAGGGGTGATGCTTCCTCTAATTTTTACACAACAGTCTTTAAAGAAAGACCTTATCTCCAGTGCATTCACATTCTACGGTGGGGGGGTTAGGACTTCAGTGTATGAATTTGCAGGGGGATACAATTCAGCCCCATAACAGGTGGGGTCTGTCAAGTCACCTACAGGTATTTATGGCTCTGGGGGGCCCTGGTATATCCCCACACAGGACAGGTTTTCTCCTCCAGCCAGCTCTTGTAAATGATGCCGTGTACCCTTCTCTTCTTTGCTGACCTGGCTCCCTGCCCCCTCCCCCAG
Seq C2 exon
CCCCCCGCTCACCCAGTTCTTCTTGGAGTGTGGAGGCCTGGTCCGCACAGACAAGAAGCCAGCCCTGTGCAAAAGTTATCAGAAGCTGGTCTCTGAGGTCTGGCACAGGAAACG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000020311:ENSBTAT00000027070:8
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.083 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0044324=UCH=PU(4.1=91.7)
A:
NA
C2:
PF0044324=UCH=FE(7.1=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:
CTCACGGGCATGAAGAACCTC
R:
CGTTTCCTGTGCCAGACCTC
Band lengths:
182-1257
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development