GgaINT0125296 @ galGal3
Intron Retention
Gene
ENSGALG00000002546 | Q90689_CHICK
Description
NA
Coordinates
chr17:8222953-8223172:+
Coord C1 exon
chr17:8222953-8223042
Coord A exon
chr17:8223043-8223118
Coord C2 exon
chr17:8223119-8223172
Length
76 bp
Sequences
Splice sites
5' ss Seq
ATTGTAAGT
5' ss Score
8.54
3' ss Seq
CTATTTTTCCCATCTTCCAGGGT
3' ss Score
10.46
Exon sequences
Seq C1 exon
GGGGACCCCGGTCCTGCTGGCCTCCCAGGGAAGGATGGTCCCCCAGGCTTGCGAGGCTTCCCTGGAGAAAGAGGTCTGCCTGGCCCCATT
Seq A exon
GTAAGTATCAACAACAGGATGCCCAGGCAGCGCAGCACACAGCTCCCCAAATGACTCTATTTTTCCCATCTTCCAG
Seq C2 exon
GGTTCTCCAGGGCTGAAAGGCAACGAAGGTCCCCCAGGCCCCCCTGGTCCTGCA
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000002546:ENSGALT00000039035:40
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(14.1=33.3),PF0139113=Collagen=PU(41.3=86.7)
A:
NA
C2:
PF0139113=Collagen=FE(24.6=100),PF0139113=Collagen=PU(2.6=11.1)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CCTCCCAGGGAAGGATGGTC
R:
GGGACCTTCGTTGCCTTTCAG
Band lengths:
103-179
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]