BtaINT0041562 @ bosTau6
Intron Retention
Gene
ENSBTAG00000013155 | COL2A1
Description
Bos taurus collagen, type II, alpha 1 (COL2A1), transcript variant 2, mRNA. [Source:RefSeq mRNA;Acc:NM_001113224]
Coordinates
chr5:32470662-32471072:+
Coord C1 exon
chr5:32470662-32470715
Coord A exon
chr5:32470716-32471018
Coord C2 exon
chr5:32471019-32471072
Length
303 bp
Sequences
Splice sites
5' ss Seq
GCTGTAAGT
5' ss Score
8.56
3' ss Seq
ACCATTGTCTTCCTCTGCAGGGA
3' ss Score
11.8
Exon sequences
Seq C1 exon
GGTCTTCCTGGCAAAGATGGTGAGACAGGTGCTGCAGGCCCCCCTGGACCCGCT
Seq A exon
GTAAGTACCCGCCCAGCCTCTCCAGGTAGCCTGTGGGCAGGGGCTTGGGGCGGCGGAGGTGGGTGGGGGGTGATGGAGCTGACAGATGTGGATCTGGGCTGATCCAGCACCCTGACCCAGCCTGAGCAGAGGCAGTGTGGACCCCGCCTGGTGGTCTGGGGTGCGGGTCACTCACTGGTGGGAGAACAGTGGGCAGTGAGGGTGGTGTTGCCTGCCGTGGGTGCCCCCTGGCCCCTCTAACCCTGGATGTGGCACCCAGGCTCTCCAGAAGCTGGCTCAGCTCACCATTGTCTTCCTCTGCAG
Seq C2 exon
GGACCAGCTGGTGAACGAGGCGAGCAGGGTGCTCCTGGGCCATCTGGGTTCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000013155:ENSBTAT00000017509:28
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:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
No suggested primer sequences
R:
No suggested primer sequences
Band lengths:
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]