BtaINT0041546 @ 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
chr5:32461689-32462074:+
Coord C1 exon
chr5:32461689-32461742
Coord A exon
chr5:32461743-32462029
Coord C2 exon
chr5:32462030-32462074
Length
287 bp
Sequences
Splice sites
5' ss Seq
AAGGTAAGG
5' ss Score
10.51
3' ss Seq
CCTCCGCATCTTTTTTCCAGGGT
3' ss Score
9.69
Exon sequences
Seq C1 exon
GGTTACCCAGGTCTAGATGGTGCTAAGGGAGAAGCTGGTGCTCCAGGTGTGAAG
Seq A exon
GTAAGGACCAAGCAGCACGTGGGCATGGGGGACGGACGATGAGGAGATGCTGCTGAGCTCAGTGGAGTTAGGACGTCTGAACAGCTTGGGTTAGGAACACCCAGCACTACAACTTAATGAATGAGCAGCAGGTCTGGAGAGCTCCGGGAATTGTCCCTCATGGAACTAAAGCTTGGAGGTGTCGGCGCTAGCTGAGATGACCAGAGCGTCCGGCTTCCTCCATGGGAATTGTCTTGCGGGCTGGCAGAGGGGGCCCTGCTCGCTGACCCTCCGCATCTTTTTTCCAG
Seq C2 exon
GGTGAGAGTGGTTCCCCAGGTGAGAACGGTTCTCCAGGCCCAATG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000013155:ENSBTAT00000017509:13
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(25.4=100),PF0139113=Collagen=PU(14.6=66.7)
A:
NA
C2:
PF0139113=Collagen=PD(11.9=53.3),PF0139113=Collagen=FE(17.1=100)
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]