BtaINT0127209 @ bosTau6
Intron Retention
Gene
ENSBTAG00000000179 | RPUSD1
Description
Bos taurus RNA pseudouridylate synthase domain containing 1 (RPUSD1), mRNA. [Source:RefSeq mRNA;Acc:NM_001075874]
Coordinates
chr25:665058-666777:-
Coord C1 exon
chr25:666676-666777
Coord A exon
chr25:666244-666675
Coord C2 exon
chr25:665058-666243
Length
432 bp
Sequences
Splice sites
5' ss Seq
CAGGTGTGT
5' ss Score
6.99
3' ss Seq
CCCCCCTCTCCTCCCCAAAGGCC
3' ss Score
10.31
Exon sequences
Seq C1 exon
GTTGTGAGAACCCAAAACCAAGTCTCACAGAGCTGGTGGTCCTGGAACACGGGCTGTATGCAGGTGACCCAGTCTCCAAAGTGCTGCTGCAGCCCCTCACAG
Seq A exon
GTGTGTCCCGGATGTGTGCCCAGGGCCCCTGCTCCCTGCTGACGATGTCCTGCCTTGGCCTCTCCCAGCACAGGGCACCACAGTGTCCCCATCCTGCAGGGGAGGAACCTGCCCGGGAGCCCCCAGCATGCTGACCAGGCTCACTCCTGCCCCCCATGCAACCTCAGAATCTGCAGCCTCTTGCCCCACACAAGGTCTCTCTGGTCTGGGTTCTCAGCTGACTGGGCGCTGCTTTGGCCCTGCCCTCACCAGCAGCGTCCCAGAAGTCGCTTCTGTTTTGAGCTCTGACTTTGTGGCACGAAGCACAGGGAGGTCTAACGTCCCCAGGGGCTGCATGAAGCTTCAAGGACAGCACTTGAGCATGATGTGAATGGGTTTGGGGTGGGCACAGGGTTGTGCTCCCACCTGACTGCCCCCCTCTCCTCCCCAAAG
Seq C2 exon
GCCGGACGCACCAGCTACGTGTGCACTGCAGCGCCCTTGGCCACCCCATTGTGGGGGACCTGACCTATGGCCACGCCTTGGGCCAGGAGGACCAGCCATTCCGTATGATGCTGCACGCCTTCTACCTGCGCATCCCCACGAGCGCCGAGTGTGTGGAGGCCTGCACGCCCGACCCCTTTGTGCCCTCCCTCGATGCCTGCTGGAGCCCTCATACCCTGCTGCAGCCGCTGGACGAGCTCGTCCAGGTCCTGCGGGCCGCCCCAGACCCTGACCCCTCAGAAGGAGGCCCTGGGCCCTGCAGCCCCTGCACGCCCCTACCTGGGCCAGGCCGGCCCCCACCACCCCCCGAGACAGAGGTGCAGCGGGCCTCCTGCCTGCAGTGGCTATCGGAGTGGACGCTGGAGCCAGACAACTGAGAGCATCATACTAGGAGGGGAACAGCAGGCTGGAACCTGCAGGGCCGGGCTGCTGGTCAGAGCCCTGGACAGTCCCTGCAGCGGCCAGGCCTAGAGCTGGGCAGCTGCGATCACAGAGGACAGGACTCTTGGGCTGCAGGACCCACACTGGCCTCCGTCCCAACACTGCTCTCCAAATGGCCTCAACAGCGCCTCCCTGGTTCTAGAGCCTCAGCTCCAAGGACTGACTTGTAGATGTGATTGGGTCAACATGCAAGAGGCAGAGCCAGGACCTGGGCCAGCCTCAGGTGGGCTCCTTCTGGCCCCCTACCCCACCCCCCAGAGCACCCTGCTGCATATTGCTCTGCCTGGACCTCCGTGCCCGCCACCCCCAGCCTGGCTGGGTCCTCCGTCTGCAGACCTCTACACCCTGACCCCCGCCCCCCGTGCCAGGCTGGTCCTACCTTGTGCCTTTGCTTCTGCCAGATTCTGGCCCCTCCACTCACATGCTGAGCGTCTCGCGTGGAAGTGGGTGTGGGCCACACACGTGCCATCAGCCCCCTCAACCCCCACCACATGTCATTCCTGCAGGCCTGCCCTGAGCATTGCCCCATGGGGTCTTCCAGGCCCCTCGTTGCAGCTGCTGCCTCTACCGCCTGCCTGACAGTCCCCAGGCAGGACCTCCGCCTGGAGCCAGGGGATCCAGGCAGTCTGTCCATCCCAACAACGCGGCCCAGCTGCAGGCCCAGCTGGGCTCTGAGAATGGAGAATAAACGCTCAGTGACAACCTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000000179:ENSBTAT00000000204:5
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.326
Domain overlap (PFAM):
C1:
PF0084917=PseudoU_synth_2=FE(20.5=100)
A:
NA
C2:
PF0084917=PseudoU_synth_2=PD(6.6=7.9)
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:
TCCTGGAACACGGGCTGTAT
R:
CTTCTGAGGGGTCAGGGTCTG
Band lengths:
345-777
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]