BtaINT0040777 @ bosTau6
Intron Retention
Gene
ENSBTAG00000000601 | COL11A2
Description
collagen, type XI, alpha 2 [Source:HGNC Symbol;Acc:HGNC:2187]
Coordinates
chr23:7305179-7305390:-
Coord C1 exon
chr23:7305346-7305390
Coord A exon
chr23:7305233-7305345
Coord C2 exon
chr23:7305179-7305232
Length
113 bp
Sequences
Splice sites
5' ss Seq
TCGGTGAGT
5' ss Score
11.11
3' ss Seq
TTCCCCTCACCTGAATGCAGGGA
3' ss Score
5.25
Exon sequences
Seq C1 exon
GGAGACGACGGAGAGATCGGGCCTCGGGGGCTGCCTGGGGAGTCG
Seq A exon
GTGAGTGTCGGGGGGGCAGGAAGTGTGGCTCGGACCCCAGAGGAGGGGCGTGGGCGTGAAAGGGATGCGCTCTCTCACATACGTGGTCCTGTCTTCCCCTCACCTGAATGCAG
Seq C2 exon
GGACCTCGAGGTCTCCTTGGCCCCAAAGGCCCTCCTGGGATTCCTGGACCCCCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000000601:ENSBTAT00000000793:20
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=FE(17.9=100),PF0139113=Collagen=FE(16.7=100)
A:
NA
C2:
PF0139113=Collagen=FE(20.2=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:
GGAGACGACGGAGAGATCGG
R:
GGGGGTCCAGGAATCCCAG
Band lengths:
98-211
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]