GgaINT0071094 @ galGal3
Intron Retention
Gene
ENSGALG00000011078 | PTPN13
Description
NA
Coordinates
chr4:47282591-47282918:-
Coord C1 exon
chr4:47282811-47282918
Coord A exon
chr4:47282723-47282810
Coord C2 exon
chr4:47282591-47282722
Length
88 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAAT
5' ss Score
6.6
3' ss Seq
AAACAAACGCTTTTGTGCAGGAC
3' ss Score
3.5
Exon sequences
Seq C1 exon
GCTTTCAGATAGTTGGTGGAGAGAAGACGGGAAAACTTGATCTGGGAATTTTCATTCACTCAGTTACTCCTGGAGGGCCAGCTGATGTGGAAGGATCTCTGAAACCAG
Seq A exon
GTGAATGGTGTGAAAAAGGAAAGGTATACATGACAGAAAAGACCAAATGAGAATGTTGGATTGTATCTAAACAAACGCTTTTGTGCAG
Seq C2 exon
GACACCGACTGATATCTGTGAACAGCACAAGTTTGGAGGGCGTCAGCCACCACACAGCATTAGAGATTATAGAGGATGCACCTGAGGATGTAACGCTCGTTATCTCTCAGCCCAAGGAAAAGCCATCCAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000011078:ENSGALT00000018046:22
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.703 A=NA C2=0.911
Domain overlap (PFAM):
C1:
PF0059519=PDZ=FE(42.9=100)
A:
NA
C2:
PF0059519=PDZ=PD(41.7=77.8)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
ACTCAGTTACTCCTGGAGGGC
R:
ATGGCTTTTCCTTGGGCTGAG
Band lengths:
177-265
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]