BtaINT0040823 @ bosTau6
Intron Retention
Gene
ENSBTAG00000000601 | COL11A2
Description
collagen, type XI, alpha 2 [Source:HGNC Symbol;Acc:HGNC:2187]
Coordinates
chr23:7293028-7293443:-
Coord C1 exon
chr23:7293390-7293443
Coord A exon
chr23:7293296-7293389
Coord C2 exon
chr23:7293028-7293295
Length
94 bp
Sequences
Splice sites
5' ss Seq
CCGGTGAGT
5' ss Score
10.9
3' ss Seq
TGACCTCATCTCTCACCCAGGGA
3' ss Score
8.15
Exon sequences
Seq C1 exon
GGCCCGGCCGGACCTAAGGGAGAGAAGGGCGTCCAGGGCCCTCCGGGACACCCG
Seq A exon
GTGAGTCACGAGGCAGGGCCCGCGTTTCTGTTGGCCCCTCTCTGTCTGGGTATTTCTCCGCGTCTCCCTCACCTTGACCTCATCTCTCACCCAG
Seq C2 exon
GGACCCCCGGGAGAGGTGATCCAGCCCCTGCCCATCCAGATGCCCAAGAAGACGCGGCGCTCAGTGGACGGAAGCCGCCTGATGCAGGAAGATGAAGCTGTGCCAACTGGGGGTGCCCCGGGTAGTCCTGGGGGCCTGGAGGAGATCTTTGGCTCCCTGGACTCCCTGCGGGAGGAGATCGAGCAAATGAGGCGGCCCATGGGGACCCAGGACAGCCCTGCTCGCACCTGCCAGGACCTGAAGCTCTGCCACCCAGAGCTGCCTGACG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000000601:ENSBTAT00000000793:62
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=0.933
Domain overlap (PFAM):
C1:
PF0139113=Collagen=FE(28.3=100)
A:
NA
C2:
PF0139113=Collagen=PD(13.3=8.9),PF0141013=COLFI=PU(41.5=30.0)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Human
(hg38)
No conservation detected
Chicken
(galGal4)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CGGACCTAAGGGAGAGAAGGG
R:
CAGGACTACCCGGGGCAC
Band lengths:
176-270
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]