DreINT0116059 @ danRer10
Intron Retention
Gene
ENSDARG00000023111 | plg
Description
plasminogen [Source:ZFIN;Acc:ZDB-GENE-030131-1411]
Coordinates
chr20:42803910-42804262:-
Coord C1 exon
chr20:42804148-42804262
Coord A exon
chr20:42804050-42804147
Coord C2 exon
chr20:42803910-42804049
Length
98 bp
Sequences
Splice sites
5' ss Seq
CAAGTATGC
5' ss Score
5.38
3' ss Seq
TCAGTCATATCTTCCCGCAGCAT
3' ss Score
8.36
Exon sequences
Seq C1 exon
AGTACTTACTGGAATGTGTAAATGGCATTGGCATGGACTACAGAGGGACAAAATCCAAGACAAAATCAGGGAAAACATGTCAGCGATGGGAGGGAACTTTCCCCCATGTACCCAA
Seq A exon
GTATGCTTCTTTATCAAATTTGTGTTTCAGGATGCTGTAAAAGACAAAATGTTTATCACAGTGAACAGCTAAATAACTTCAGTCATATCTTCCCGCAG
Seq C2 exon
CATAACACCAAGAGCTTACCCAAAAGCAGATTTGGAGTCCAACTTTTGTCGAAACCCAGATGGAGATAAGGGGGGTCCCTGGTGCTACACCACAGATCCTGAGAAACGATGGGAGCACTGCAATATCCAAGACTGCACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000023111:ENSDART00000045816:5
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:
PF0002421=PAN_1=PD(1.3=2.6),PF0005113=Kringle=PU(41.8=84.6)
A:
NA
C2:
PF0005113=Kringle=PD(57.0=93.8)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AAACATGTCAGCGATGGGAGG
R:
ATTGCAGTGCTCCCATCGTTT
Band lengths:
167-265
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]