GgaINT0079541 @ galGal3
Intron Retention
Gene
ENSGALG00000020084 | CAPN13
Description
NA
Coordinates
chr3:7790645-7790858:+
Coord C1 exon
chr3:7790645-7790681
Coord A exon
chr3:7790682-7790783
Coord C2 exon
chr3:7790784-7790858
Length
102 bp
Sequences
Splice sites
5' ss Seq
ATGGTAAGA
5' ss Score
9.48
3' ss Seq
TAAAATGGGTATGCATCCAGGGA
3' ss Score
2.44
Exon sequences
Seq C1 exon
GAACTCAAACTCTCAGCTCAACCCAGCGCCGCCAATG
Seq A exon
GTAAGAGTCCATGGAAACTGATACTGGTGGTGGTAAGCAGGGGGGAAAGCGTTTCAAAGACAACTGATTCTTGCAATGTCTGTAAAATGGGTATGCATCCAG
Seq C2 exon
GGAGGAAAGAGGGAGAAACTGATCTAAACTCCACAGCTCAGTATAGCCGTTTTCAAAAGACTTCACACCTGAGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000020084:ENSGALT00000014759:17
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=1.000 A=NA C2=0.538
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Human
(hg38)
No conservation detected
Human
(hg19)
No conservation detected
Mouse
(mm9)
No conservation detected
Cow
(bosTau6)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AAACTCTCAGCTCAACCCAGC
R:
CTCTCAGGTGTGAAGTCTTTTGA
Band lengths:
106-208
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]