BtaINT0112944 @ bosTau6
Intron Retention
Gene
ENSBTAG00000001244 | PLAT
Description
Bos taurus plasminogen activator, tissue (PLAT), mRNA. [Source:RefSeq mRNA;Acc:NM_174146]
Coordinates
chr27:36738833-36741390:-
Coord C1 exon
chr27:36741224-36741390
Coord A exon
chr27:36739668-36741223
Coord C2 exon
chr27:36738833-36739667
Length
1556 bp
Sequences
Splice sites
5' ss Seq
CAGGTAAGC
5' ss Score
9.88
3' ss Seq
ACCTCTTCTCCCTTCTGCAGGGT
3' ss Score
12.67
Exon sequences
Seq C1 exon
CTTCTCCGTTCTTTTCCGAGCGGCTGAAGGAGGCTCACGTCAGGTTGTACCCATCCAGCCGCTGCACTTCCCAACACTTGTTTAACAGGACCGTCACCAACAACATGCTGTGTGCCGGAGACACACGGAGCGGTGGGGACCACACAAACCTGCACGATGCCTGCCAG
Seq A exon
GTAAGCGCCGGCGGGTCTCTTCTCCTGAGCACCCCCCATCCAAGGGCTAAAGTGTTCCTCAGCCAACTGGTTCCTAACCAAGAAAAAAAAGTTACAGCCAGAAAGCAGTGATTCATCTGGGGCGGGGGATGGGATCTAGATGAGAGCCTCAGAGAATAAAGCAACTGGAGCCAAGATCAAAGTCACCCAAACTGAAGACATCTAAACGGCAGTAAATTTCCCCAATGTCTGCACCGGAACCCCCGCCTGGTACAGGATTTCCTGTAAGCCCAGGCAATTAAACAACTATCAAAGTGATGGATAAAGCCACACAAGTTAAGACAGCTTTGGTTTATGTGGGTGCTGGGGAATCAGGGTCTCTTGGTAGCGTGGGAGGAACGGCAGCTTCCTGGAAATAGGAGAGAGATGATCTGTGAGAAAGAAATTTTAGGAACTTGAATTCAGCCCTCTGATGAGTTTTCCCCCTGGGAAAGCACACCATTACAGGGTCTCTGGGTTGGCGTCCCCATCAGAGCTGGTACATACCTGTATTTCATGATAACTCTGAGTGTAAGACACAGACCAGTGTAAGGTAGGACCTAATGGAGCAAAGGAACCCTCAACGCGGGGCTGTTTTCACGTCCACTGTGCTGCGGGCTCTCACTGAGGCTGGGGGACGGGGGCGTGGCTGGAGGCAGTGGGGCTGCGCACTCCCACTGAGGAGTGCCCAGTTCTGATGCGGGGATCACACCCGCATCTCCTCCTCTTGCCTACGTGACAGCCTTTGGTCTCTTTTTGAAAGGTTTTCTCAGACACCTCCACCACCTAGCTCGACAGTCATAAAAGGTTGTGTGCAAAGTGAAACCGTGATCTATCAGCCAGCGTCAAGTTAAAAACAAGTCAATTCAATTAAATAAGACAATAACAGCTAATGATTGCCAAGAGTTCTACTCAATGCCCTACATTGTTCTCAGGAGCTTTTCAAGCTTTCTTCCAGTTAATTCCCATAACCTCATAAGGGAAGTACTATGATTTCTGTTTTAGATCATTATTACTTAGTATCATTCAGGTAAGAATACTGAAGTCCAGTGGCCTAGGGCCGCACAGCTAGTGGTAGCTTTACCACCCGGTGGGGATGAGGTATCGCTAGTGGTAAAGAATTTGCCTCCCAGTGCAGCAGACGCAGGAGACCTGGGCTCGATCCCTGGGTTGGGAAGTTCCCCTGGAGAAAGAAATGGTAACCCACTCCAGGATTCTTGCCTGGAAAAAGCCCATGGACAGAGGAGGCTTGCAGGCTACTGTCCATGTGATTGGAAAGAGTCGGACATGACTGAGCACTTGTCAGCAATGTCTGAGCTCAAGTCCACTTTACAACAAAACTACAACCGAATTCTGTAATGGTCCAAGATTGGGGAGGTAAAATTTCCCTCCCTGAAACTGAGCACGTTGAAGGATACATATTAGTGCCTCATATTAGTGGTACGTAGAATACATATCAGCACTACAAATATTCACCCTAACATCCCCGCAAAGAGTCTGCACTTTTGCACACAGCTGACCTCTTCTCCCTTCTGCAG
Seq C2 exon
GGTGACTCGGGCGGCCCCCTGGTGTGTATGAAGGACAACCACATGACCTTGGTCGGCATCATCAGCTGGGGCCTGGGCTGCGGGCGGAAGGACGTCCCGGGCGTGTACACCAAGGTGACTAACTACCTGGACTGGATCCGAGACAACACTCGCCCATGACCAGGGACACCTGTTTCCCACTACGTCACAGAGACCCCGCTTCTCCCACCTCTGAAGACTCACCACGGCAGGGCCTTCTTCACACAGCGGAAGTTGGGGGAGGGTGTAGTTTCACAGGTACTTTTCCATTTTGGAAGTTTTCAGGGCTTAAGGGCTGAACTGTACTGTCAGACGGGAAGATGGATAAATGCCAGTCCCTCGTGGAAAACCACTCCCCAGGGCGGAAGCCCGCTTCCTCCTCTATGCACACGAGCGTCTTTGGAAAGGGGACCACAAAGATGAAAGCATGTCTCAGTAGGCAAAGATAACTCGAGCCTTCGGGAAAGAAGGGTTAGACGTATTCTACTAGGAATAGAATGTCTATTTATAGTCCCAAGGAAGCCCAGCAGGAACCTCCTACCAGGGGATGGGCTGGCTGGCCAGACCACGTTCCTCGACTCCAGCCCTTAAGTCAAGTGTTGGGCTCTCCTTTTGCAGCTCTTGGAGGGAATCCTGTTGTGTATAGTGTAATTCTCTTTCTTTATATGTTTCATGATAGAACCAGGAGACACGTATCATTTTAATAACTGATAAACTAGGCTCTCGCATATTTATATCAGTTCATTTTTGTTTGTACTCTGTTGCCACTACCTGTATGATACCGTACTGGAATAATAAATTCTGATATATTTTTCAC
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000001244:ENSBTAT00000001642:14
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.089 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0008921=Trypsin=FE(22.4=100)
A:
NA
C2:
PF0008921=Trypsin=PD(18.3=84.9)
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:
AACAGGACCGTCACCAACAAC
R:
ACTACACCCTCCCCCAACTTC
Band lengths:
353-1909
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]