BtaINT0112952 @ bosTau6
Intron Retention
Gene
ENSBTAG00000001244 | PLAT
Description
Bos taurus plasminogen activator, tissue (PLAT), mRNA. [Source:RefSeq mRNA;Acc:NM_174146]
Coordinates
chr27:36743091-36743820:-
Coord C1 exon
chr27:36743735-36743820
Coord A exon
chr27:36743287-36743734
Coord C2 exon
chr27:36743091-36743286
Length
448 bp
Sequences
Splice sites
5' ss Seq
GCGGTAAGG
5' ss Score
9.63
3' ss Seq
CTCTGTCCTCCCCTCCGCAGTCA
3' ss Score
11.29
Exon sequences
Seq C1 exon
GAATCCCGATGGGGACGCCCAGCCTTGGTGCCACGTGTGGAAGGACCGCCAGCTGACCTGGGAGTACTGTGATGTGCCCCAGTGCG
Seq A exon
GTAAGGCCAGCTCCCCTTACCCAGCATTATTCTTGCCCGTGTCCTCCGCCGCTTCCCACATCTGGGAAGCTGTCTGGTTCAGGCTACGCAGCTGCCCGCTTTTCAGGAAGGCTGGACCTGGGTGGGGAGGGGGCTTGCCCGGCTGGAGCCATGGTGGATGGCGATGCTGTTGGGCAGGTGATGGGAGGGGCAGGAGAAAGGAAAGGATGCAGCCATTTCTCATGGATGGCATCGGGCTCCAGGCTGCTCTCTGGAGATGCCTTGTTAGTAGTGATGGCAGCCGGGATGCGGGGAGGAGGGAAGCAGAGGCTCCATCACTCTGTACAGATGCTGCAGAAGCGCAGCCGTGGGTGGAAACCTGGGTTCCCAGACGAGACACTGGCCTGGGGCTTGGGGACCTCGCCCAGGCCCACAGGTCTGAAACTGCGCTCTGTCCTCCCCTCCGCAG
Seq C2 exon
TCACCTGTGGCCTGAGACAGTACAAGCGGCCCCAGTTCCGCATCAAAGGAGGCCTCTTCGCGGACATCACCTCCCACCCCTGGCAGGCCGCGATCTTCGTCAAGAACAGGCGGTCCCCGGGAGAGCGGTTTCTGTGTGGGGGGATCCTGATCAGCTCCTGCTGGGTGCTGTCGGCCGCCCACTGCTTCCAGGAGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000001244:ENSBTAT00000001642:9
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=0.000
Domain overlap (PFAM):
C1:
PF0005113=Kringle=PD(34.1=93.3)
A:
NA
C2:
PF0008921=Trypsin=PU(20.7=77.3)
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:
CAGCCTTGGTGCCACGTG
R:
CTCTCCTGGAAGCAGTGGGC
Band lengths:
263-711
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]