GgaINT0004936 @ galGal3
Intron Retention
Gene
ENSGALG00000003215 | PEF1
Description
NA
Coordinates
chrUn_random:12599162-12599487:-
Coord C1 exon
chrUn_random:12599443-12599487
Coord A exon
chrUn_random:12599351-12599442
Coord C2 exon
chrUn_random:12599162-12599350
Length
92 bp
Sequences
Splice sites
5' ss Seq
AAGGTGAGA
5' ss Score
8.68
3' ss Seq
GCTTGTCTGTGTCCCCTCAGGGT
3' ss Score
11.46
Exon sequences
Seq C1 exon
GGCCCCCCAGGAAAGCCTGGCACTGCAGGACCTGCTGGCCAGAAG
Seq A exon
GTGAGAGTTGTCAGAGCTCCCCCATGGTGCCCCCAGCTCCACACCACACCAGGGGTGCCATGGTGAAACTCTGCTTGTCTGTGTCCCCTCAG
Seq C2 exon
GGTGAAGCCGGGTCCCCTGGAATGCGAGGGTACCCTGGGGAGAAGGGCCGTGCTGGCGCGCCTGGGGGGCCGGGGAAGAGTGGCTCCATGGGCCCCATAGGGCTGCGGGGTCCTGCAGGAGAGAGGGGTCCCCCCGGCTCACCAGGACCTGCGGGCAGCCCTGGGCTGCCAGGACCCCCCGGGATGATG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000003215:ENSGALT00000005093:6
Average complexity
IR
Mappability confidence:
NA
Protein Impact
5' UTR
No structure available
Features
Disorder rate (Iupred):
C1=NA A=NA C2=1.000
Domain overlap (PFAM):
C1:
NA
A:
NA
C2:
PF0139113=Collagen=PU(88.5=96.4)
Main Inclusion Isoform:
NA
Main Skipping Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GGAAAGCCTGGCACTGCAG
R:
GGACCCCTCTCTCCTGCAG
Band lengths:
167-259
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]