DreINT0115259 @ danRer10
Intron Retention
Gene
ENSDARG00000062707 | plat
Description
plasminogen activator, tissue [Source:ZFIN;Acc:ZDB-GENE-081104-181]
Coordinates
chr8:2202369-2204218:-
Coord C1 exon
chr8:2204070-2204218
Coord A exon
chr8:2202670-2204069
Coord C2 exon
chr8:2202369-2202669
Length
1400 bp
Sequences
Splice sites
5' ss Seq
AAGGTAAAG
5' ss Score
9.06
3' ss Seq
ATAACCTTGATCTTCTTCAGGGG
3' ss Score
8.04
Exon sequences
Seq C1 exon
TTTCTCCGTTTTACTCAGAGAGGATCAAGCGTGGTCTGGTGCGTCTGTGGCCGCAGGATCAGTGTGTCCCTGAAAAACTGTCTGGTCGACTGGTCACCTCAAACATGCTGTGCGCTGGAGACACCCGAGGGCTGGACGATGCCTGCAAG
Seq A exon
GTAAAGTTAAGAATCTCCACAACCAGCGCAGAGCCTTGGAGATCAAATCTGAATCGACCTCCCCCAGATCCAATTCTCATTATTTAAAGGGCCATGAAACCCTCTCGTTTCAGCAGGGTGTTTTCACACCTCTACTTTGGAAAAAGTCAGAAAAGTGGGCGTGTCCAGCTCTGTTTAGGGGGGAGTGTCGGAGGAACTAAAGTGGGATGGTGTGGGAGTGTCTATTTGGGCACGCGCGAGTTTCAGAGTCAAAATACACACACACACACACACACACACACACATACAGCAGAAAGTGATGGTGTTTAACCTACATGGACATCTGTAGTCGAATTATTTGGCAAATTATTAAATGGTGGACTTTAACTGCAGTTTGGCTCTTTCATTCAGGGAATTCATTCATGCCCCTCACGACAAACGAGATATTTGATTCGAGGAGCTGCTCTAAGCGTGTATTTTTCATGCAATGTTTGATACCGCACGGCGAATGAGAGAAAAAAAAACTCAGCATTTCCCAGAAACTTAGATGCACACGGCAGGTAGTGTCAGAAAGCCGCGTGTGTTATTCCGGTCACTAAATGCGGTGAAAATCCTACACGAGGTTAAAGTTTGGTTGTGGTGCTAACGTGTTTACACTCTGTGCAATAGTTTGTTAGATACGAACAAACTGAATAAACAAAGAGCACTGGTCGCTCACTTACCAAATCTGTAGAGACAGGACAATCACCAGCAACTAGAGCCGCGTCTTTATTAAGAGGAGACGAGCAGCGAATCCGGATCTCAGCGTTTGCAGATGAGAACAGCTCTCAGGTAAACAATAATCCTCCTTAGACACGTGAGTCATTGTTGTCGCGCGTCGCGTACACTGTTAATCCACACGTGAGTCTGAGCTCTCACAGAGAGAAAATGAAAACAAAACTTCACTGCAGCAAACTATAAAAGCAACACTTCACGCTTGTTTTGCCAACACAACGTGGCGTCTCTGTCCTGAAAACACGGTGATAGTAATGAATATTAATGAAGTTGCACAATAGAGCGCGCTGATTGGTTTGAACCAAGCCTTACTCATGCATTAATGCAGCACACTGTAAGACGTAATAAGACTCACTCTGGCACAGGCGTCCAGTCTGCACGCTGGAATACACGCTATTATGTCATGACCGTGACGCAGCTTCAAAAATTCGTTTCAAACAGGAAGTACGAATTTGCTTGAAATAACGCAAAAACAACCAATTTACACTTTTTAGTGAAATATAGGTGTCCTAATAGTGTTTATAGCAGTGTGGGACACATATACCACTGTCAACAGCTCAAAAAATGTGTTTTGGTGTTTCGTGACCCTTTAAGTTAACTAAATAGCTTAATTCTTCGTTTACTAAAATAACCTTGATCTTCTTCAG
Seq C2 exon
GGGGATTCTGGTGGTCCTCTGGTGTGTCAGAAGAACGGCAGGATGACTCTGATGGGTTTGATCAGCTGGGGCGACGGCTGTGGGAAAAAGGACACGCCTGGAGTTTACACACGCGTCACCAAATACACAAATTGGATCTCCAGCAAGATGAGCGCAAACTAAGACAAGCGCAGACAGAAAGTCATGTGCTGGAGGAAAAAACATCACATTCACCAACCTGCTGGAGTGTTTGTGACTGAAGGAGGACAACATCTGAGAGTTTGTGAGTTTTTGCACACCGGACTGCACATCTGAATCCAAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000062707:ENSDART00000147275:14
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0008921=Trypsin=FE(20.4=100)
A:
NA
C2:
PF0008921=Trypsin=PD(18.8=83.3)
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:
AACTGTCTGGTCGACTGGTCA
R:
TCCGGTGTGCAAAAACTCACA
Band lengths:
356-1756
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]