GgaINT0135997 @ galGal4
Intron Retention
Gene
ENSGALG00000003709 | PLAT
Description
plasminogen activator, tissue [Source:HGNC Symbol;Acc:HGNC:9051]
Coordinates
chr22:2709386-2711255:-
Coord C1 exon
chr22:2711115-2711255
Coord A exon
chr22:2709535-2711114
Coord C2 exon
chr22:2709386-2709534
Length
1580 bp
Sequences
Splice sites
5' ss Seq
AATGTAAGT
5' ss Score
8.62
3' ss Seq
TATATTCACATCCCTTTCAGTTT
3' ss Score
8.03
Exon sequences
Seq C1 exon
CTCTGCTGCAGTTGAACTCGGACACAGAAGACTGTGCTATTGAAACAGACACTGTTCGAGCAGCCTGCCTCCCAACACCTGACCTGCAGCTGCCTGACTGGACTGAATGTGAGATCTCTGGTTATGGTAGAAACGAAGAAT
Seq A exon
GTAAGTAGAAGATGTGTTGTGGCCAAAGCCAGGTTCTCTGCCCCAAAGAATTCAAGCCTTTAGCCCTGTTTAATCTGTGACTCCTGAATTATTTCATGAAATTATATTAGCACTCCAAAAATGTACCTATATGTGGAACATACATTAAAAACAAGTTTTTTCATTCATCTGAGATATGTCAGCTGCCTGGGTTAGCAGAGTTTTTCTTGAAACTCTCAAACAGTAGGAACACAGAAAATGGCAAGATGAATAAGACAAAGTTTGTCAGTGAAGGCTTCTGCATTTCTGCTGTACTATTTATTGTATTTAATTATTAACTTAGATATTGTCATTCTCAAAGAAATCAATTTCTGTCAAGATTTAATACCATGCATAATAATACCATGTAGTTGTGGGTAGTGGGCATTAATCCAAAACATACATTGACTGTACAGCAATTAGCAATAAAAAAAAAAAAAGCTAAGGATGTAAAAGTCCTGGATATATATTAAAAGGTCAGCCAAATTAAACAGAATAGTTAAATTGGTTCAATTGAGCAGTACCTACAAAGGTCATGAAGTCCAACTGCCTGGCCACTTTGGTGCTAACCAAAAGTTACAGTACAGTATTTTGATTATGCCCTCAATACTTCCTGAACAGGCATACAGTATCAACCCCCTCACCAGGAATGGTTTTGAAACAGAGCTACTTTAAAAACCAGAGTCAAGAAAAAGCCTGGAATAAAACCTGTCTGGAAGTACATATAGACTAACCTGTATTCCAAAAAAGAAGAAAAAGCAGCTTATAAATGCCTTATTGGCATTTATTTTTATTATCTTTAAATTGTAAATGCTGAGGCAGAGACTGTGAAGCATCCATCATAACAAGGACAAATCACAATTTGAGCTATTAAGGCTTTTGTGACAGAGTTAACATACAACTTTAACAGACAAGTGTATCACAAAATGTTTTAAAAGAGCTAAACCTAGTGCTTCTTTTTCTATAGGGAGTACAGTTAACTCTTTCAGAGCAAAAGTACACTGCAATTATAATTTAAAACCAGACTGAAAAACAGTCCTGCCAATTTTCAGCTTTGTGCAGTTGCAACTATGCAGAAGAATAAAACCGACATGCAAGGCAGATATAAATCAATTCCATTCCAAGATAACGAGTGTGCATTCCTATCTAGTTATTCAGTATTTTGTACAAGACAGCTGTTTTTAACTAACCCAAATCTAATACTAAGAGTCAGGATCCCTTTTCATACATGTATTGATTATTAGATGCGCTCCATTTAGATTGATGTCATTCATGCAAAGACAACCCCCTAAGAAACCTAGCAATTTGCACCCTGTAAAAATCTCTAACACTTAAGCTTACTGAAGCAGCAAAATTGTCTTTCAACGGTATTTAAGTTGTTCTCACCGGCAAAGCAGAACGCCCATAACTAAAAAAAAAAGACTCCTGGCAAGGAAATATTAGTTTTCCCACCCTCCTCTCCTGCCACTAGTTAATGCACTCTCCCAAACTGCAGAAACTGAACTGCAAAGTTTTATACATATATACTCATGTATATTCATATATATTCACATCCCTTTCAG
Seq C2 exon
TTTCTCCCTTTTATTCAGAGCACCTGAAGGTAGGCCACGTCAGACTATTTCCAGCCAGTCGGTGCACCACACAGCATCTACACAACCGGACAGTTACAGACAACATGTTATGTGCAGGAGACACAAGGCACCTTGATGATGCTTGTAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000003709:ENSGALT00000005886:12
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:
PF0008921=Trypsin=FE(19.6=100)
A:
NA
C2:
PF0008921=Trypsin=FE(20.4=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CTCTGCTGCAGTTGAACTCGG
R:
ACAAGCATCATCAAGGTGCCT
Band lengths:
287-1867
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]