BtaINT0112943 @ bosTau6
Intron Retention
Gene
ENSBTAG00000001244 | PLAT
Description
Bos taurus plasminogen activator, tissue (PLAT), mRNA. [Source:RefSeq mRNA;Acc:NM_174146]
Coordinates
chr27:36741224-36742724:-
Coord C1 exon
chr27:36742584-36742724
Coord A exon
chr27:36741391-36742583
Coord C2 exon
chr27:36741224-36741390
Length
1193 bp
Sequences
Splice sites
5' ss Seq
CCTGTGAGT
5' ss Score
7.21
3' ss Seq
GTCTTCCTGTTCTCTTTCAGCTT
3' ss Score
12.06
Exon sequences
Seq C1 exon
CGCTGCTGCACCTGAAATCAGACTCGCTGACCTGCGCCCGGGAGAGTGCCTCTGTCCGCACCATCTGCCTCCCAGACGCCAGCCTGCAGCTGCCCGACTGGACGGAGTGCGAGCTGTCCGGCTACGGGAAACACGAGTCCT
Seq A exon
GTGAGTGGGAGGAAGTCGCTGTGCCATCCTGTCTGTCTGGGGGCAGCGTCGGGGGCGGGTGCTGACCAGAGAGAGGAAAGAGCGGTCCTGAGAGTGTCCAGTCCAGCCCCGGGGCAGGCTCTGCCACTATGATAGTCTGGGCAAGTTCCTGCTAAGTGAAGCCCCGCCATCCACCTTCCCAGCCAATGGCCCAGTCGGTCAAGAGAGAGGTCTGAGTGGCAGGAGAGCTTTAAGGGCTGAAGATTTCAAGGAGGTTTCGATAAGACATGGAGCGAGCTTAGTTAAGGGTGCGGTTCCTAAACTCTGCCTGCCACCCAGCAGCCCTCACCCTGCGCCTGGTGAGCCCTGTGATCCAGGCGTGGATTTTTCATTTCATGTTGCTCCAAGCCTCAGTTTCCTCATTGGTAAGAATGAATAGATTGTATGAGGCTTAAATGAGATATTAGGTTAAACCAGTGGTTCTCAGCTAGGGTGCTCTTGCCTGCTAGGCAACATGTGGCAATGTCAGTTATTGTGACGACCCAGGATGGAGGTTTATACCCACATTTAGTGAGTAGAAGCCAGTGAAGCTTCCTGGTGGCTCAGATCGTAAAGAATCCACCTGCATTGCGGAAGACCCTGGTTTGATCCCTGGGTCGGGAAGATCCCCCGGAGAAGGGCATGGCAACCCACTCCAGTATTCTTGCCTGGAGAATCCCATGGACAGAGGGGCTTGGTGGCTATAGTCCACGGGGTTGCAAAGAGTCAGACATGACTGAGGGACTAAGCACGCGCGCACAAAAGCCAGGGATGCTGACAGACATCCGCAATACACAGTGCAGCCCCTGCAAAACCTGTTCAGTTCAGTTCAGTTCAGTCACTCAGTCGTGTCCGACTCTTTGCGACCCCATGACTCGCAGCACGCCACGCCTCCCTGCCCATCACCATCTCCCGGAGTTCACTGTTATCTGGCCCCAAATGGCACTTGTGCTGCTCTTGAGAAACCCTGGGTGAAACTCTATGAAATTGCCAGAGTTTGCCCACCCTTCTGCAGGTCAAAAGGGTAATATATTGGCAATTTCGTAGGATTCAACTTAATACACGTAAAAGATTAATCAGTATTAGCTATCATCACAAAGTTCAGCTTTCTCCTTCCAAAAGGTTTCTAAATAACTTTCCCTAAAGTCACAAGCTGTCTTCCTGTTCTCTTTCAG
Seq C2 exon
CTTCTCCGTTCTTTTCCGAGCGGCTGAAGGAGGCTCACGTCAGGTTGTACCCATCCAGCCGCTGCACTTCCCAACACTTGTTTAACAGGACCGTCACCAACAACATGCTGTGTGCCGGAGACACACGGAGCGGTGGGGACCACACAAACCTGCACGATGCCTGCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000001244:ENSBTAT00000001642:13
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=0.089
Domain overlap (PFAM):
C1:
PF0008921=Trypsin=FE(19.1=100)
A:
NA
C2:
PF0008921=Trypsin=FE(22.4=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:
TGCACCTGAAATCAGACTCGC
R:
CTGGCAGGCATCGTGCAG
Band lengths:
302-1495
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]