BtaINT0158397 @ bosTau6
Intron Retention
Gene
ENSBTAG00000020311 | USP20
Description
Bos taurus ubiquitin specific peptidase 20 (USP20), mRNA. [Source:RefSeq mRNA;Acc:NM_001105333]
Coordinates
chr11:100250303-100255417:+
Coord C1 exon
chr11:100250303-100250399
Coord A exon
chr11:100250400-100255363
Coord C2 exon
chr11:100255364-100255417
Length
4964 bp
Sequences
Splice sites
5' ss Seq
AAGGTAAAG
5' ss Score
9.06
3' ss Seq
TCTTTCCCCGCCTCACACAGAGC
3' ss Score
7.47
Exon sequences
Seq C1 exon
GTGAGCCCGGGCCAGCATGGGGGACTCCAGGGACCTTTGTCCTCATCTTGACTCGATAGGGGAGGTGACCAAAGAGGACTTGCTGCTCAAATCCAAG
Seq A exon
GTAAAGGGTCAGACTTTCCGGGACCGAGGCCCACACCCAGGGCATCCCCCGCCTCCACCACATTCCTGGGATACAGACATTTCTGAAGCCGCGGAAGCACTGGCTCCCAGCAGTCTCAGCTTGGCCTTTTATGTAAATGGAAAAGCTGGCGTCTGTTCAGGAGGCCTTCCGGGGCTGCGTCCTAACAGCCATTAATTACCACGTAGACCATCCATTTGGGAGCGCTGATGCCCATTAGTGGCTGGAGCAGGTGCAAGGCGGAGAGTCAGGCTCCGAGAGTCCACGGGCTTTTTGCACACTTGACCTGAGGAGGGCTCAGGGAGGTTCAAAGAGAAGAGGTGGGCCTCTGTTTTTTTTTTTTTTTTTTTGTCTATACTGTGGCTTGCAGGGTCTTCGTTCCCTGACCAGGGATCCAACCCGTGCCCCCTGCAGTGGAAGCTTGGAGTCCTGACCGTGGGACCCCCAGGGGACTCCCAAAGGTGGGCCACACTGAGTAGGGAGGATGTGCTATTTGTCTGTTTGTTAGATTAAAAACAATTTAAGTAGGTAACGCTTTCACATGGTTCAAACTGAAATGATGTAAGAAGAAAAATGTCAGGGAGTCCCCCTCCCACCCGTCCTGTGCTCACCCTCTCCATCCCACCCTCCAGACAGCCACGAACGTTGGTTTCTTTTGTATCTTTTCAGAGTTTGCTTATGGGAATACTTATTTTTCATTTCCCCTCTATTACATAGAAAGCAGTGTACTGTAGCTGTTTTGGTAACGTGCTCTGTTCGCCTGGCAGAGTATCTTGGAGCTCTGTGGTCTCAGCACATGGGTCTCGTGGTCTGTCTTAAAGCTGCATCATAGTTCACTGTGTAGACTCCGCAGCCGATCCTCTGTGGGTGGACATCTGGGCGCTTTGCAGCATTCTGTCTGTACAGTGTCCTCGTGTTCAGGGGCAGGGCCGTGTGGAGGGGCCATTCCCAGGGGTGGGGTTGGGTCAGACTCCTAGACAGATTCCTGTGTCTTCTTTCCAGGCACCTAATGCTGGTTATTCAGCCTCCCTGCACCAGCAGGTGCTGGGTGGCTTCTGGCCTGAGCTGGCTCAGTCTCAGGTGTGATTCTTCAAAGTTCCTGTGGCTTCTTTTGAAGTCGTCTGCTACTGAACCAGGTTCATCTGCTGATTCATAGCAAGCCAAACGCTGAGACACCGAAGTTTGCAGCAAAGAAAGGGTTGATTCACAAGTGAGGAAACAGGAGAACAAGCCTCAGATCAGCCTCCCAGAAGGCGAGGGTCTTGGAATATTTATGGGATGAAGAAGCAGGATGGTCTTAGGCATGGGGAGAGATGAGGTCATCAGTGTTCTGCACAAGTGTGTCTGAGTTATGTGCTTCTTCCTAGGATGCGTGTTCAAAAATGGAGGTGCTTAGCATGATCTGAGGCTGAAGTCTTGGGCCCTTTGACATCAAAATGTCATTTATCAGACACTTACACACACCCAGTTTTAGGGTCAGTGGTCCCAAACAGTCTTAGCCGGCTCGAACTGGACAAGACTCCAAGTTTCTGAAAAAACAGCTTAGACCCCTATTACTATGGCAACGTATACATCAGAGCTGTTATCTGTAGGGGTGATTAAGGAGTCTTGTGATGTATAGGCTAGGGGTTTTTTACCCAGCTGTTCCCTTAGTTGCTGTTGTGTAAGACAAGTTCCATTTCTGTTCATCACCAGTTTCTGCTAACCCTGTAGAGGATGGTTTCAGTGTGGTCAGGAGGAAGAGCAGAGCAAGGCTGTGGTGCATTTGCCCCATCTAACACTGGTCTCTTCCTGCGTCTGCACAAAGGAATAAGTGAAACAAACTGAGAGTTTCTTGGGAAATCTGAGAGCAGGGAGGAGACGAACAAGGTGGGAAGAGGGAGGCAGAACTTGGGAAGATCGGGCTGGGACATGGCAGCCTTTTGGAAATCTACAAAATGAAACCAACGTGGTTTTAAAATACCCAGAAGGTGCAAGGATTGAGCCGGGTAGCTCACAATGGAGGCAATGCAAGTGGCTGAGAAACTCTTGAAAAAAGGTGCTTGATTTCCCTGGTGGTCAAGGATTTGGCCAGGAAACCAACATGGCACCGTTTCAGACGCGCACGGCACAAACTGCTGTCACTCAGGGATAGGGAGGAGGGGCGTGGACCCGACGTTTGCAGTCAAGTTACCGTGACTGCAGGGGTTCAGTTCCCGTGCTCGGAATGTGTCTAGGAGCAGTGTATGTACCAGTTACAAGACACAAATACAGCAGTGTTTACTGAGCATTCTTTGTAAAAGGAAAACACTGGTGGTCAAACGCATATCTACCAGGAAGGGAATGAGTGAAACAGTTGTGGCGTCTGTACCCGCAGTGTGGGCCCCCGTGTACTTATCTCAAAGAATGAGATGGGGATCTCTGTATACAGACACACAAGGGTGACCCTAAGTAGGTGACAGAAGCCTGTTACTGAGAAGTGTGTACAGTGTGATCTCATTTTTACTAGCCAAAGGTATGGAGGGAAATACTTCAAGTTATTACAGCATGTATATATTATATATAATACACTACATATTATGTACAGCATATATGTAATATGTGATACATTATGTACAGCATACATATATACAATATATGACACATATACAGCATATATGTACTATATATAATATATGACACATTATATGCAGCATATATGTATTATATGCAATATAGGACACATTACATACAGCATATATATACTATATATAATATATGACACACATATAGCATGTATTATATATAATATACTACATATTATATACAGTGTATATGTGTTGTATGTAATATGCTACATATTATATACAGCGTATGCGTCATTTAAGTTGTTGAAATAAGCACATAATACTTTTATCATTCATATGACTGAAATGAAAAAACAAATTTGGGAAGATGGGAGTGAACTGTGAAATCAGAAAGTCACAAAAGAGATGACAAATTTGGAAAGGTCAGGAGTAGCAACTTTGAGTCTATCGAGCAGACTGGTCTCCTGCCCCCTTAGCATCCTTGGCAAGAGACCCTAAGACACAGACTGCAAACCTCAGCCCCACTGATGGGATGAGCTGCGCCTTCTCAACCTTGCTGAGAGAGCCATGTTCAGGATTTTTACAAACACAGCCAGAATCTGGGCTTAGTGGAAAGAAGTTCCCATGGAGGCCTAAGGGTCGATGTGGCCACCCTTGGGAGGAGACTAGACCTTTCCCGTAAGTCTGATGACCCTGACTCCTCAGCTGATAGTGCTTCTGACAGTAGGGTCATGACCTCTCCAAACCTCCATTTCTCATCTGTAAGAAGGGGGTCTTGGGACCTATTGCAGAGACTGTGATAAGGATTACATGAGCAAGGTCCAAAGAACTTAGCTGGATACCTGGCTCATTATGATCCCTCACCAGGGATCAGCTCTGTAACTGCTGCAGAGACCAGTGCTTAGAATTCATCTCACAACTGGCAGAGACACACTGGGTATTGTGAAAGCTCAGCTGGAAACTGCTGTTCTAGAGAGGCACAGAGAAAATTACTTAGGACAGTTTAAATTATAATGAAAAGACCTTGAAATATAGTGAGTTAAATGAGATAGGAGTTTGCTTTTCTCATTGAGCAGTCCAGATGTAGGTAGCTCTGATAGAGTGGATCTGTCATTCTCAACACATGCCTTTCACCTCCAGGTCCAAAGTGGTTACTTGAGTTCCTGCCATCACATCTGCATTCCAGCCAATGGAAACAGGAGAGAGACCAAGGGTTGTGCAAAACTCAGAAGTGGCACATGTCACTTTTACTGTTACGCTATCGACTAGAACCGAGTCCCATGATCACAGTGGGGGCTAGGACACATAGTCTTTAGCTCACTGACCATGTGCTCAGCCAAAATACGTAGATTCTTTTATTAAAGCAGGGAAGAGAGATATCAGTGGACCAGAAGCAGGCTCTGTCATCCTGATCAACAGATACCTGGGTGTTTCTGTGGTCAACAAATATACTGATCTGATTTGTACCATACTCTGTGAAGTCGCAGGGGTAGGCAAAACAGACCATCCCTCCTTCATGGAGCCCATAGTCTAGCCGGGCAGAAAGGCTTAAATAAATGAGTGTCATAAAGGAACTGGCAGTCCGGAGTTGATGATAAGAACGTGCAAGAGAGAAAGAGGCTGATATTCCCTGGTTTACGCAGAGAACCAATAAAGCTCTTGACACAGGGCTTGTATTGCTCATGAAGGCACAGGGCACCCTCTCAAGAGGCTGAAGGCACAGGGCGCCTTCTCTAGGGAGTCTTGGAAACCCGGGCAGGAGAGTAAGCGCGACGGGTTTCTGCGCTCCATCAAATTAGCCGGAGAGAGAGAGAGAGAGAAAGAAAGAAAGAAAGACACGGGGACCCAAGCTCTGATGGAGCAGAGTGCTTTAATGGTCTTTCTGTGAGTATATATAGGCTATGGTACAAGAAATTTCTTTCAACAATGATAAAGATCAGAAAACCAAAAGTACAACAACCGTTACCAAGGGAACAAGGGATAATAATGGTCACAAGGTCAGGAGACAATCCATATCCAAGAGAGAGGATCGAGACTGGGCAGTTTTGTCTTAAGGAGAATGTTTACTGAAGGAGATTCAAGCCTGTCTCATCGTATGACCTCAGTCCTGAGAGCTGCGTGCAGTTCTACTCGCTTCTGGCAGAAGCTGATAAGCAACAGAGGATTTATGAGAAACAGCACGTAGGAATCCTCCTGTTAAACATTCCCTGATAAGCTTTAAGTGATTGTATTGAAAATGTTTTTTCAGGCACATGAAAAAAACAAAATTCGAACAGTAAAGCTTAAAGTGGCCCCGTGGGCTGGAATCTCTGTGAGGCAAAGCCTCTGGGCTGAGTCTGATGGCTCATGTCCTGTGGCCACTCACACCCTCCTCTTGGTCTCTTTCCCCGCCTCACACAG
Seq C2 exon
AGCACCTGTCAGTCATGCGGGGTTTCTGGACCCAACCTGTGGGCCTGTCTCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000020311:ENSBTAT00000027070:3
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0214814=zf-UBP=PU(23.1=83.3)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Chicken
(galGal4)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
No suggested primer sequences
R:
No suggested primer sequences
Band lengths:
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development