BtaINT0112950 @ bosTau6
Intron Retention
Gene
ENSBTAG00000001244 | PLAT
Description
Bos taurus plasminogen activator, tissue (PLAT), mRNA. [Source:RefSeq mRNA;Acc:NM_174146]
Coordinates
chr27:36744201-36745794:-
Coord C1 exon
chr27:36745703-36745794
Coord A exon
chr27:36744382-36745702
Coord C2 exon
chr27:36744201-36744381
Length
1321 bp
Sequences
Splice sites
5' ss Seq
AGGGTAAGT
5' ss Score
10.45
3' ss Seq
TTGGATTTCCTGCGTTCCAGTTG
3' ss Score
6.47
Exon sequences
Seq C1 exon
AAACCCGGACCAAGACTCAAAGCCCTGGTGCTACGTCTTCAAGGCAGGGAAATACATCTCTGAGTTCTGCAGCACTCCAGCCTGCGCTAAGG
Seq A exon
GTAAGTGCAGCCTCCCCAGGGCCCCTACGGCCTCACGGAGTCCCAGGGGGGTGGGGTGGGGAAGGGAGATCTGGAGGACAAGGCTGATGGTCCTTCTGCAAATGAAGAGACAAAGGAGAGAATTGGTCAGTCACTTTGGCATCAGAGGAAGGAAGTCAAGAGGCTTAGGTCCTCATCAGGCTTGGCCTCTAACTAGCTGTTTGACCTGGAGCCACTCTCTGCACCCCGCTGACCCTCAGTTTCCTTGTGGACAGAGAAGATGGGGCTCTACCGGTGGTTTCCAGGCCTTTTGGGAGTGTGCAAGTTCTCTCTTGTTTGATTAATTGGCCTATTTCTCAAGATCTCGCTCTGTCTCTGAAGACTTTTAATGTGAGAAAATTTCCCAGATTTAAAAAGTACTCAGCTACAAAAAGGCACCATGAGTTCACTGGTGCTTTCCAAAATAATGATGCTATTTAATCACAAGTGTAAAAATATGTTTCAAAGTTCTAAATATACATGTATAAAAATGCACATTCAGGCTAAAAGTGATGCTGATAGACTTGTGAATTTGAGAGCTCTTTAGAATAACTTTAATCCTGGAGAAGGGAAGAGCTACCCACTCCAGTATTCTTGCCTGGAGAATCCCTGTGGACAGAGGAGCCTGGTGGGCTACAGTCTATGGGGTCGCACAGAGTCGGACACGACTGAGCGACTAAGCAGAGCACAGCACAGTGTAACTCTAAAGCATTGGCATAAACTGGGACTCACTGGTACCGATGCTCTCAAAGGCCCCTCCTCACTGGGTTACTGGTGCCTGCCAGTGTCCTGTGTCAGTTTCGAATGCGGAGAAAAGAGGGTAATATAGGGGCAAATATGCAGTATCCGAAGGTTCATACTCTTGCTTCCCTCCCAAGTCCAATAAATCCTTCAAGGCCCTGGCAGACAAAATCCGAGAAAACTGGGCCAGCCCACATGTCCCCCCACAGAAGACCCCAGGTTGACAGCAACCTGTCAAGTAGAAACAAGGAAACCCTTAACAGCCTTCCAGGCAGCTCTAATCAATCCCCACTAGCTGAACTGGGCAGCCTTTCCTGAACCTGAATATCCCTCAGAGTCTCCCTTAACACAGCCCAGTGATGGGGGGGCTGGCACCAGATGGAACCGCTGACCACCCTGAGCAAAAGCATTTGAAGGAGAGTAAAGGCCCAGGTGGGCAGGCTGGCCTCCCCGCCCCGGGAGCCCCAAGCCACAGCCCCAGGCTTCAGGCCCTGCTGCAAACCCTACTTGCTGCTTGGGCACTTCAGCGGCTGTGTTTCAGTTTGGATTTCCTGCGTTCCAG
Seq C2 exon
TTGCAGAAGAAGATGGGGACTGCTACACTGGAAACGGGCTGGCGTACCGCGGCACCCGCAGCCACACCAAGTCTGGGGCTTCCTGCCTCCCGTGGAATTCCGTGTTCCTAACCAGCAAGATTTATACCGCCTGGAAGAGCAACGCGCCGGCCCTGGGCCTGGGGAAGCACAACCACTGCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000001244:ENSBTAT00000001642:7
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=87.5)
A:
NA
C2:
PF0005113=Kringle=PU(64.6=86.9)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AAACCCGGACCAAGACTCAAA
R:
CAGTGGTTGTGCTTCCCCAG
Band lengths:
270-1591
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]