GgaINT0028819 @ galGal4
Intron Retention
Gene
ENSGALG00000006725 | ACAN
Description
aggrecan core protein precursor [Source:RefSeq peptide;Acc:NP_990286]
Coordinates
chr10:12563222-12563786:-
Coord C1 exon
chr10:12563612-12563786
Coord A exon
chr10:12563350-12563611
Coord C2 exon
chr10:12563222-12563349
Length
262 bp
Sequences
Splice sites
5' ss Seq
CAGGTAAGG
5' ss Score
11.08
3' ss Seq
CTATGCACCTTGTCCCACAGGTA
3' ss Score
10.13
Exon sequences
Seq C1 exon
GCGTCGTGTTCCACTACAGAGCAATCTCCACAAGGTACACTTTGAACTTCGAGAGGGCAAAGCAGGCCTGTATCCAGAACAGTGCTGTCATTGCCACCCCTGAGCAGCTGCAGGCTGCCTACGAGGATGGGTACGAGCAGTGCGATGCCGGCTGGCTGGCTGATCAGACTGTCAG
Seq A exon
GTAAGGGGAGATAAAAGCCACTTTAGGGAAGGGTTATTGTAACAAAGCCACTGATGGAGGATGGTTGAGAAGCAGTTGGGAAATGCTAAGAAAATCCACAAGTGTGGCTCAACCACGCTGAGCCCTGTGTCCCCCATTAGTGGGCACCTTGGCCTCTGATGGCTTTGGCTGGTTCTCAGGTCTGTCACAGGGAAAGCAGGACGTTAGCTCCTCCAGCCCTGTGCTGCTGCCCCATCCTGCTTCTATGCACCTTGTCCCACAG
Seq C2 exon
GTACCCCATCCATCTGCCCCGGGAGCGCTGCTACGGTGACAAGGATGAGTTTCCAGGAGTGAGAACCTACGGTGTCCGTGAGACAGATGAAACCTATGATGTTTACTGCTATGCAGAGCAAATGCAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000006725:ENSGALT00000010881:3
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:
PF0019312=Xlink=PU(60.4=98.3)
A:
NA
C2:
PF0019312=Xlink=PD(38.5=84.1),PF0019312=Xlink=PU(0.1=0.0)
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:
CGTCGTGTTCCACTACAGAGC
R:
TGCATAGCAGTAAACATCATAGGT
Band lengths:
289-551
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]