DreINT0115264 @ danRer10
Intron Retention
Gene
ENSDARG00000062707 | plat
Description
plasminogen activator, tissue [Source:ZFIN;Acc:ZDB-GENE-081104-181]
Coordinates
chr8:2219591-2220372:-
Coord C1 exon
chr8:2220198-2220372
Coord A exon
chr8:2219683-2220197
Coord C2 exon
chr8:2219591-2219682
Length
515 bp
Sequences
Splice sites
5' ss Seq
CAGGTGCTG
5' ss Score
4.87
3' ss Seq
CTTTGTGTTTTATTGATCAGGAA
3' ss Score
8.63
Exon sequences
Seq C1 exon
ATACTCTTGAGAGATGCTCCAGAGGTCAGGGGTTGGGATATCGAGGCTCGTGGAGCGTCAGTTCGTCAGGAATGGAGTGTATTAACTGGAACTCCAGCTCTCTGCGAGGGAAGAAGTTCACTGCGAGGAGACCAGAGGCGAGCACACTGGGTCTGGGGAACCACAACTACTGCAG
Seq A exon
GTGCTGGAGCTGGAGCTCACGCTGTATTCTTAATGCATGCACTTACGCCCCATTTACACGGGGCTTCAGCGCCAATGCGTGACTGAAGGCGTGTCTGAAGTTGGGGCTGAAGCGATCGTCATAGAAGCGTCAGCCAATGAAATTCAGTCAGCAATAGGCCAATGTCTAGCTGGTGTATTTGCATACAGCAATCTGATTGGTTGACGCTTCCGACAACGCTTGAAAAGTTGAGTTAGTCCCAACTTCTACAGTGAGCAACGCCTCTGAAGCGGCGCCGACGGATCCACAATGCAGACGCCCCGTGTGAATGGGGCATTACTGACCAAACATTGATATGTGTGTTAGGGATGCACAATACTGGGGATCATATTTTCAACATCTTACTTAATAAGTGCTAATAAACAATTAACATCTTGATAATAGGCAGGAAATAAGCCTGTAGTTAATGCTGTGACCATTATTATAATGCTTATTTAAGATTATATGAATAATTTGCTTTGTGTTTTATTGATCAG
Seq C2 exon
GAATCCAGACGGAGACTCTAAACCTTGGTGTTATGTATATAAAAAGGCTCAGATCTCATGGGAGTTTTGCTCTTTACCGACATGTGTAATAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000062707:ENSDART00000147275:6
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=PU(64.6=89.8)
A:
NA
C2:
PF0005113=Kringle=PD(34.1=87.5)
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:
ACTCTTGAGAGATGCTCCAGAGG
R:
TTACACATGTCGGTAAAGAGCA
Band lengths:
262-777
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]