GgaINT0046110 @ galGal3
Intron Retention
Gene
ENSGALG00000002552 | COL3A1
Description
NA
Coordinates
chr7:581398-581703:-
Coord C1 exon
chr7:581605-581703
Coord A exon
chr7:581452-581604
Coord C2 exon
chr7:581398-581451
Length
153 bp
Sequences
Splice sites
5' ss Seq
GAGGTTAGT
5' ss Score
7.15
3' ss Seq
TGATCTTTCTCTTTTGTAAGGGT
3' ss Score
6.7
Exon sequences
Seq C1 exon
GGTAATCAGGGTGAACCTGGCCGTTCTGGTCCACCTGGCCCAGCAGGCCCACGTGGTCAGCCAGGTGTAATGGGTTTTCCTGGTCCAAAAGGAAATGAG
Seq A exon
GTTAGTGGGCTGTTTCCACTTCTCCTGTGCTTATGCTTGAGCAGTCATGTGGTAAAATTATATTGCTTCATGGGAGATTCAATGCTGCAGTTGTTAAGTTATTGTGTGTGGACTAGAACAAGTATTTTACATGTGATCTTTCTCTTTTGTAAG
Seq C2 exon
GGTGCACCAGGTAAGAATGGAGAAAGAGGCCCTGGTGGACCACCTGGAACTCCT
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000002552:ENSGALT00000004033:27
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=1.000 A=NA C2=1.000
Domain overlap (PFAM):
C1:
PF0139113=Collagen=PU(14.5=90.0)
A:
NA
C2:
PF0139113=Collagen=PD(7.6=27.8)
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:
GTGAACCTGGCCGTTCTGG
R:
AGGAGTTCCAGGTGGTCCAC
Band lengths:
143-296
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]