BtaINT0127208 @ bosTau6
Intron Retention
Gene
ENSBTAG00000000179 | RPUSD1
Description
Bos taurus RNA pseudouridylate synthase domain containing 1 (RPUSD1), mRNA. [Source:RefSeq mRNA;Acc:NM_001075874]
Coordinates
chr25:666676-667050:-
Coord C1 exon
chr25:666948-667050
Coord A exon
chr25:666778-666947
Coord C2 exon
chr25:666676-666777
Length
170 bp
Sequences
Splice sites
5' ss Seq
AGGGTACGG
5' ss Score
7.86
3' ss Seq
GCTTGCCTCGCTCCCCTCAGGTT
3' ss Score
9.81
Exon sequences
Seq C1 exon
GTGCGGGGGCACGTCCAGGAGAGCCGAATGACCATCAGCTACGCCATCGGCAAGAACAGCACAGAAGGCCGGACCCACACCATGTGCATTGAAGGCACACAGG
Seq A exon
GTACGGAGGGCAGGGGGTGGAGGGACCAGGGACACAGCCGTCCAGAGGGGACCCTGGATGAGCTGGGGCAACCAGGCCACATGACCGGGCTGCAGTGGACTCGGCCCCGGAGTGGCCTAACCCTAACCCTAACCCCAGCTATCTCTCTGAGCTTGCCTCGCTCCCCTCAG
Seq C2 exon
GTTGTGAGAACCCAAAACCAAGTCTCACAGAGCTGGTGGTCCTGGAACACGGGCTGTATGCAGGTGACCCAGTCTCCAAAGTGCTGCTGCAGCCCCTCACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000000179:ENSBTAT00000000204:4
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.114 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0084917=PseudoU_synth_2=FE(20.5=100)
A:
NA
C2:
PF0084917=PseudoU_synth_2=FE(20.5=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:
CGTCCAGGAGAGCCGAATGA
R:
CTGTGAGGGGCTGCAGCA
Band lengths:
194-364
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]