BtaINT0113939 @ bosTau6
Intron Retention
Gene
ENSBTAG00000001271 | PLG
Description
Bos taurus plasminogen (PLG), mRNA. [Source:RefSeq mRNA;Acc:NM_173951]
Coordinates
chr9:98048858-98051100:-
Coord C1 exon
chr9:98050961-98051100
Coord A exon
chr9:98048979-98050960
Coord C2 exon
chr9:98048858-98048978
Length
1982 bp
Sequences
Splice sites
5' ss Seq
AAGGTCAGG
5' ss Score
6.23
3' ss Seq
TTCCTTTCTGTTCTTCCCAGATA
3' ss Score
10.49
Exon sequences
Seq C1 exon
GTTTTCGCCTGAAAAATTTCCTCTAGCGGGACTGGAGGAGAACTATTGCAGGAATCCAGACAATGATGAGAATGGGCCCTGGTGTTACACCACAGATCCAGACAAGAGATATGACTACTGTGACATTCCCGAATGTGAAG
Seq A exon
GTCAGGGATGGCTCTAGAAAAAGTTTTCCTATTCTTGCCTTTATGTATGGAGTAATTTGCTATAAATTGATTATCTGTGGGGATATTAGTAATCAATTAGTGCTGTGTTTGACGTCATCAAGTAATACATGACCTCTGGGAAAAGACCAAAATTTTGCAGAATTTCCATTATGGATCTAAATTATCTTTATTAACATGTAGTTCAGGGTTCGGGGTGGGGAACGCATGTGTGCCTGTGGCGGATTCATTTTGATGTTTGGCAAAACTAATACAGTTATGTAAAGTTTAAAAATAAAATAAAATTAAATAAATTAAAAAATTAAAAAAAAAAAACCATGTAGTTCAACAGGGACAAATATAAAACGAGTCGCCAGTCCAGGTTCGATGCACGGTACTGGATGCTTGGGGCTGGTGCACTGGGATGACCCAGAGGGAGGGTAGGGGAGGGAAGAGGGAGGAGGGTTCAGGATGGGGAACATGGGTATACCTGTGGCGGATTCATTTCGATATTTGGCAAAACTAATACAATATTGGAAAGTTTAAAAATAAAATAAAATTTAAAAAAAAAGTTAAAAAAAAAACAGAACTAGATGTAAACTCTAGATGCACACTTCTTATGCTTAAAGCTGTGACACAGTTTAAGCCAGAAACATATTTGCAATTCAACTGCTAGCATAAAACCACAAAATCAATACAATTCAAACACACAACATTAAGTTAACAGGGTAGACTTTGTCATGTTGTTGAAACCAAGCCATGAACCAGTTTTTAAGTCAGCCATCTATTGTTTTAATGGAACAACCAATTTAAGAGCTCACTTCAAAAGTCAACGTCAAAAGAATGTAAAATATCCTATGGGAAAATGTTCTTTACTTCATATTTCCTGCTACATTTATTGATGCAATAGGGGGATGAATGAAGGTGGGGTTTGCATAACCATGTGGTTGAGTCCATACTGGCTCAGTTTCCCATCACTTCCTCTAGTCCAACCTTTGGCATTCTTTATTTATTTGTACACCATGTTATGAGGTCATCTGGCCCTTTACTGACATGCGAGTATCCTTTTTATATCAAGTCTGCTTCTGTTTTCCTTATTGTCACATAAAAATTCAAGTCGTATATTCTTCTGCTATACCACATTATATTAAGCATTGCAACGTTTCCATTTTACAGGGATGCAAGAAAGAAAAACAACCAGTCATGCTTCTCAATAATAATGATAAAAAGAGAAGCATTGTCCCTTTAGGTGAATATTGTTTCTCTCTTGAGGTCACGAACACAAGCAAAAACCCTGGCAGTAAAATTCTGAGAGGCTGCCGGCTTCTTCGGCAGTTATCCAGACAGAGAGAGCTTCCCAATGGCTTGATGGGAAAGAATCTGGCTGCCAATGCAGGAGACACAGGAGATGCGGGTTCCATCCCTGGGTTGGGAAGATCCCCTGGAGGAGGAAATGGCAACTCACTCTAGTATTCTCGCCTGGAAAATTCCATGGACAGAGGAGCCTGGCAGGCTACAGTTTACGAGGTCACAAAGAGCAGGACGTGACTGAGCAAGCATGCATTCAATCAGAATAATTCCACAGGAATTTTTTGGAAGACAGACCTCAAATATTAAAAAAATTCTAGTAGAGAATTTACAGATTCCTGAGATTATATGCAATCTCTCCCCACAACCACCAAGAACCAACACATGTAGCAACCTTGAAGACAAAGCATTATGGAGTTTCTGGATTTGGTCACAACTGTAATAGTAGAGAAGGTATAGACCACATCTGCTAATTCTACCATTTGAAAAAGAGAATGACGTTTTAGATTGTATTAGAAAATTAAGCCTTTATTGCCAATTTTGTTGCTAGGTAATTGGTGGAAAATTACCAACGAACAAGTGGTAAAGGTATTTGAGACACTTCTAGTGATAGTCTAGTCTTTACCCTTTTTTGCTTCATTCATTTCCATTTCTTTCTTCCTTTCTGTTCTTCCCAG
Seq C2 exon
ATAAATGTATGCATTGCAGTGGAGAAAACTATGAGGGCAAGATTGCCAAGACCATGTCTGGACGTGACTGCCAGGCTTGGGACTCTCAGAGCCCACATGCCCACGGATACATTCCTTCCAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000001271:ENSBTAT00000053284:5
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.021 A=NA C2=0.146
Domain overlap (PFAM):
C1:
PF0005113=Kringle=PD(57.0=93.8)
A:
NA
C2:
PF0005113=Kringle=PU(48.7=92.7)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Chicken
(galGal4)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CGCCTGAAAAATTTCCTCTAGCG
R:
AATGTATCCGTGGGCATGTGG
Band lengths:
248-2230
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]