GgaINT0046103 @ galGal3
Intron Retention
Gene
ENSGALG00000002552 | COL3A1
Description
NA
Coordinates
chr7:586567-586819:-
Coord C1 exon
chr7:586775-586819
Coord A exon
chr7:586666-586774
Coord C2 exon
chr7:586567-586665
Length
109 bp
Sequences
Splice sites
5' ss Seq
ATGGTAAGT
5' ss Score
11.01
3' ss Seq
TCCCCTTTGGCTCTCCACAGGGA
3' ss Score
11.59
Exon sequences
Seq C1 exon
GGTCCTCCTGGAAGAGCTGGAAGCCCCGGCAACAAGGGTGAAATG
Seq A exon
GTAAGTACTTTTCACATCAATGTATTTTGCTGCGCTGTGTTAATGAGGACTTGGCAGAATCCAGCCATGTGGAGCTCTGTTAATCCTGATCCCCTTTGGCTCTCCACAG
Seq C2 exon
GGACCTTCTGGGATTCCTGGTGCTCCTGGTCTTCCAGGAGGCCGTGGTCTTCCTGGTCCTCCTGGTACAAGTGGAAACCCTGGAGCAAAAGGCACTCCT
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000002552:ENSGALT00000004033:20
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=PD(6.9=26.7),PF0139113=Collagen=FE(17.9=100)
A:
NA
C2:
PF0139113=Collagen=FE(41.0=100),PF0139113=Collagen=PU(22.1=51.5)
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:
GTCCTCCTGGAAGAGCTGGAA
R:
TGCCTTTTGCTCCAGGGTTTC
Band lengths:
138-247
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]