BtaINT0040773 @ bosTau6
Intron Retention
Gene
ENSBTAG00000000601 | COL11A2
Description
collagen, type XI, alpha 2 [Source:HGNC Symbol;Acc:HGNC:2187]
Coordinates
chr23:7305771-7306007:-
Coord C1 exon
chr23:7305954-7306007
Coord A exon
chr23:7305825-7305953
Coord C2 exon
chr23:7305771-7305824
Length
129 bp
Sequences
Splice sites
5' ss Seq
AAGGTAACA
5' ss Score
8.92
3' ss Seq
GCTGCCCCTCTCCTCCTTAGGGT
3' ss Score
10.47
Exon sequences
Seq C1 exon
GGCCGAGCGGGTGCTGACGGAGCCCGAGGGATGCCTGGGGAACCTGGAGTGAAG
Seq A exon
GTAACAGGCTTGGGCCCCTTTCTGGTGCCCACCCGGAACTCATCTGTTTCCTGGGGATAGCCCCGCCCCGCTCATGACGTGATGGGAAAGGGGCGGGCACCTCACCTGGGCTGCCCCTCTCCTCCTTAG
Seq C2 exon
GGTGACCGAGGATTTGATGGCCTTCCGGGGCTGCCTGGGGAGAAGGGACACAGA
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000000601:ENSBTAT00000000793:17
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(12.9=44.4),PF0139113=Collagen=FE(21.8=100)
A:
NA
C2:
PF0139113=Collagen=FE(21.8=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CGAGGGATGCCTGGGGAA
R:
TCTGTGTCCCTTCTCCCCAG
Band lengths:
84-213
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]