GgaINT0097662 @ galGal3
Intron Retention
Gene
ENSGALG00000009641 | COL1A2
Description
NA
Coordinates
chr2:23542926-23543133:+
Coord C1 exon
chr2:23542926-23542979
Coord A exon
chr2:23542980-23543088
Coord C2 exon
chr2:23543089-23543133
Length
109 bp
Sequences
Splice sites
5' ss Seq
GCTGTAAGT
5' ss Score
8.56
3' ss Seq
ACTATGTTCTCTGCTTACAGGGT
3' ss Score
9.43
Exon sequences
Seq C1 exon
GGTGCTCGCGGTCTCCCTGGTGAGAGAGGAAGAATAGGTGCCCCTGGACCAGCT
Seq A exon
GTAAGTGGCTTCCCATCTGTCTGTTGGTACTAATGACCAGCCACTTACCGTGGCTTTCTCTGATGGTTGACTCTTTCCTGTCTCTACTCACTATGTTCTCTGCTTACAG
Seq C2 exon
GGTGCTCGTGGGAGTGATGGCAGCGCTGGCCCCACTGGACCTGCA
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000009641:ENSGALT00000015706:13
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=FE(21.8=100)
A:
NA
C2:
PF0139113=Collagen=FE(17.9=100),PF0139113=Collagen=PU(2.4=13.3)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GTGCTCGCGGTCTCCCTG
R:
CCAGCGCTGCCATCACTC
Band lengths:
82-191
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]