BtaINT0041557 @ 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
chr5:32468921-32469153:+
Coord C1 exon
chr5:32468921-32468974
Coord A exon
chr5:32468975-32469054
Coord C2 exon
chr5:32469055-32469153
Length
80 bp
Sequences
Splice sites
5' ss Seq
AAGGTGAGC
5' ss Score
9.6
3' ss Seq
CGCTGCCTCCTCTTGTATAGGGA
3' ss Score
7.95
Exon sequences
Seq C1 exon
GGCGCTCCTGGAAACCGTGGTTTCCCAGGTCAGGATGGTCTGGCAGGTCCCAAG
Seq A exon
GTGAGCAGGGGAACAGGGACTGGGCCCACCCATCACCAGTCAAATGGCTTTCTGCTGACCCGCTGCCTCCTCTTGTATAG
Seq C2 exon
GGAGCCCCTGGAGAGCGAGGACCCAGTGGCCTCGCTGGTCCCAAAGGCGCCAACGGTGACCCTGGCCGTCCCGGAGAGCCTGGCCTTCCTGGAGCCCGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000013155:ENSBTAT00000017509:23
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(22.4=100),PF0139113=Collagen=FE(25.8=100),PF0139113=Collagen=PU(12.8=61.1)
A:
NA
C2:
PF0139113=Collagen=PD(11.8=27.3),PF0139113=Collagen=PD(43.9=87.9),PF0139113=Collagen=FE(37.2=100),PF0139113=Collagen=PU(2.8=6.1)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GGCGCTCCTGGAAACCGT
R:
GGGCTCCAGGAAGGCCAG
Band lengths:
151-231
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]