GgaINT0010858 @ galGal3
Intron Retention
Gene
ENSGALG00000005628 | COL9A3
Description
NA
Coordinates
chr20:8355182-8355481:+
Coord C1 exon
chr20:8355182-8355214
Coord A exon
chr20:8355215-8355334
Coord C2 exon
chr20:8355335-8355481
Length
120 bp
Sequences
Splice sites
5' ss Seq
GAGGTATGT
5' ss Score
9.81
3' ss Seq
ATTATTTTTCTTTATTATAGCCA
3' ss Score
7.4
Exon sequences
Seq C1 exon
GGTCCCTTTGGTCCTCCCGGCCAAAAAGGAGAG
Seq A exon
GTATGTGTCAGGTACTGCGGACTCGTGCCCTGTAACATTTGCTTATAAACATGCTTACTGTATCTTTCAGTGATGGATCTCCTTAAACTTTAAGTGCTGCATTATTTTTCTTTATTATAG
Seq C2 exon
CCAGGAAAAAGAGGAGAACTGGGTCCAAAAGGTGCTCAAGGACCCAATGGGACAGCTGGAGCTCCAGGGATCCCAGGACACCCAGGGCCCATGGGCCATCAGGGGGAGCAGGGCGTTCCTGGCATCACAGGCAAACCGGGGCCTCCT
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000005628:ENSGALT00000009029:27
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=1.000 A=NA C2=1.000
Domain overlap (PFAM):
C1:
PF0139113=Collagen=PU(11.1=63.6)
A:
NA
C2:
PF0139113=Collagen=FE(76.2=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GGTCCCTTTGGTCCTCCCG
R:
GGTTTGCCTGTGATGCCAGG
Band lengths:
170-290
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]