BtaINT0040799 @ bosTau6
Intron Retention
Gene
ENSBTAG00000000601 | COL11A2
Description
collagen, type XI, alpha 2 [Source:HGNC Symbol;Acc:HGNC:2187]
Coordinates
chr23:7299280-7299599:-
Coord C1 exon
chr23:7299510-7299599
Coord A exon
chr23:7299334-7299509
Coord C2 exon
chr23:7299280-7299333
Length
176 bp
Sequences
Splice sites
5' ss Seq
GCTGTGAGT
5' ss Score
7.39
3' ss Seq
CCCCAATCTCTGGCTCACAGGGC
3' ss Score
6.83
Exon sequences
Seq C1 exon
GGCGATCCCGGACCCCCTGGGGCCCCGGGGAAGGATGGTCCCGCTGGTCTGAGGGGCTTTCCGGGAGAGAGAGGCCTCCCTGGCACTGCT
Seq A exon
GTGAGTGTGACCCCGACCCAGATGCCTGTGAAGAGGCCCCGCACCTCCTGGCTCCCCAGCGTCACCCTGCGCCCACGTCCCAGCCCCCACCCTTCCCCGCGTGTCTCCTAAGCTCCGGGCCTGTGAGGTCCCCCTCTTCCGTCTCACGTCTGTTATCCCCAATCTCTGGCTCACAG
Seq C2 exon
GGCGGGCCTGGTCTGAAGGGGAATGAAGGCCCGGCTGGTCCCCCAGGCCCTGCA
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000000601:ENSBTAT00000000793:40
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(32.2=100),PF0139113=Collagen=FE(36.2=100)
A:
NA
C2:
PF0139113=Collagen=PD(2.2=11.1),PF0139113=Collagen=FE(21.2=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Chicken
(galGal4)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CCCCGGGGAAGGATGGTC
R:
CCAGCCGGGCCTTCATTC
Band lengths:
106-282
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]