BtaINT0041564 @ 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
chr5:32457375-32457541:+
Coord C1 exon
chr5:32457375-32457407
Coord A exon
chr5:32457408-32457508
Coord C2 exon
chr5:32457509-32457541
Length
101 bp
Sequences
Splice sites
5' ss Seq
GACGTGAGT
5' ss Score
9.22
3' ss Seq
TGTGGGTGTCTCTCTCACAGATC
3' ss Score
11.61
Exon sequences
Seq C1 exon
GGACAGAAAGGAGAACCTGGAGATATCAAGGAC
Seq A exon
GTGAGTACACTTTCTACTCCCATGTTGCATCGACTTTTCTAACTGGGTCATTTCCTTGAGGTCTCTTCTAACTTGCCGTTTTGTGGGTGTCTCTCTCACAG
Seq C2 exon
ATCGTAGGACCCAAGGGACCTCCTGGACCTCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000013155:ENSBTAT00000017509:3
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(11.2=100)
A:
NA
C2:
PF0139113=Collagen=PU(13.6=81.8)
Main Inclusion Isoform:
NA
Other Inclusion 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:
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]