BtaINT0042455 @ bosTau6
Intron Retention
Gene
ENSBTAG00000015581 | COL9A3
Description
collagen, type IX, alpha 3 [Source:HGNC Symbol;Acc:HGNC:2219]
Coordinates
chr13:55027389-55027606:-
Coord C1 exon
chr13:55027562-55027606
Coord A exon
chr13:55027443-55027561
Coord C2 exon
chr13:55027389-55027442
Length
119 bp
Sequences
Splice sites
5' ss Seq
CTGGTACGT
5' ss Score
9.57
3' ss Seq
GGTTCACCCCTCCCCCGCAGGGC
3' ss Score
9.09
Exon sequences
Seq C1 exon
GGTCTCCCCGGACGAGCAGGGTCCAAGGGTGAGAAAGGAGAACTG
Seq A exon
GTACGTGGTTGCTTTCTCCAGGAGAGGGAGAGGGGAAGGTGCAGCCGCAGTCTGGGTCCTGGGGGCAGAGGGGGCCCTCCCCTGCAGGCAGGCACTCAGGGTTCACCCCTCCCCCGCAG
Seq C2 exon
GGCAGACCTGGAGAGCTGGGTGAGGCCGGCCCCTCGGGAGAGCCTGGTGTCCCT
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000015581:ENSBTAT00000020699:20
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(0.1=0.0),PF0139113=Collagen=FE(20.9=100)
A:
NA
C2:
PF0139113=Collagen=FE(25.4=100),PF0139113=Collagen=PU(18.4=77.8)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GTCTCCCCGGACGAGCAG
R:
AGGGACACCAGGCTCTCC
Band lengths:
98-217
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development