BtaINT0041320 @ bosTau6
Intron Retention
Gene
ENSBTAG00000004582 | COL20A1
Description
collagen, type XX, alpha 1 [Source:HGNC Symbol;Acc:HGNC:14670]
Coordinates
chr13:54740039-54740367:-
Coord C1 exon
chr13:54740209-54740367
Coord A exon
chr13:54740120-54740208
Coord C2 exon
chr13:54740039-54740119
Length
89 bp
Sequences
Splice sites
5' ss Seq
TCGGTGAGC
5' ss Score
9.1
3' ss Seq
CCCCTCTCTCTTCCTCTCCGAAG
3' ss Score
1.75
Exon sequences
Seq C1 exon
GTGCATGTGGCCGTGGGCCGAGCCAGGGTCAGGCTCTACGTGGACTGCCGGAAGGTGGCCGAGAGGCCCATCGGGGAGGCCGGCGGCCTGCCTGCTGCCGGCTTCGTCATGCTGGGCAGGTTGGCCAAAGCCCGGGGCCCCCGGAGCAGCTCCGCCTCG
Seq A exon
GTGAGCCAGACCATCTGGGGCTGGTGGGCCCCTCCCACCCCCTGTGACAGCCACACCTGACCAACCCCACCCCTCTCTCTTCCTCTCCG
Seq C2 exon
AAGTTCCAGCTCCAGGTGCTACAGCTCGTGTGCAATGACTCGTGGGCAGAGGAGGACAGGTGCTGTGAGCTCCCAGCATCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000004582:ENSBTAT00000065814:24
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.013 A=NA C2=0.037
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Rat
(rn6)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GGTCAGGCTCTACGTGGACT
R:
GAGTCATTGCACACGAGCTGT
Band lengths:
174-263
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development