BtaINT0041554 @ 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
chr5:32467615-32467940:+
Coord C1 exon
chr5:32467615-32467713
Coord A exon
chr5:32467714-32467886
Coord C2 exon
chr5:32467887-32467940
Length
173 bp
Sequences
Splice sites
5' ss Seq
ACGGTAAGA
5' ss Score
10.65
3' ss Seq
TGCTTTTCTCCTTTGTTAAGGGT
3' ss Score
7.96
Exon sequences
Seq C1 exon
GGTGCCCCTGGCATTGCTGGTGCTCCCGGCTTCCCTGGACCCCGTGGTCCACCCGGCCCTCAAGGTGCAACTGGTCCTCTGGGCCCAAAAGGTCAAACG
Seq A exon
GTAAGATCCAGTGAACCCCGAGTCCCACCCACAGCCCCAGAGTCAAACCTGCCACCCCTACCTCCTGTGCCCACAGAGTCCTCTAGTGGGCTGCCTTTAAGGTGGGGTGGCGGAGGACTTCTAGGGCCGTGGGGAGAACGGAGTGTAAGAACCTGCTTTTCTCCTTTGTTAAG
Seq C2 exon
GGTGAGCCTGGTATTGCTGGCTTCAAAGGCGAACAAGGCCCCAAGGGAGAACCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000013155:ENSBTAT00000017509:20
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(35.2=100)
A:
NA
C2:
PF0139113=Collagen=FE(18.7=100),PF0139113=Collagen=PU(14.5=61.1)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CCCCTGGCATTGCTGGTG
R:
TTCTCCCTTGGGGCCTTGTTC
Band lengths:
146-319
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]