BtaINT0041318 @ bosTau6
Intron Retention
Gene
ENSBTAG00000004582 | COL20A1
Description
collagen, type XX, alpha 1 [Source:HGNC Symbol;Acc:HGNC:14670]
Coordinates
chr13:54740784-54741134:-
Coord C1 exon
chr13:54740992-54741134
Coord A exon
chr13:54740894-54740991
Coord C2 exon
chr13:54740784-54740893
Length
98 bp
Sequences
Splice sites
5' ss Seq
ACGGTCAGT
5' ss Score
8.02
3' ss Seq
ATTCTTGTCGCATCCCCCAGCCG
3' ss Score
5.88
Exon sequences
Seq C1 exon
CGACATCCACCTGGCCACCCTGCCCCCGGAGCACACAGTCGTCTTCCTCCTGCGCCTGCTCCCTGAGACTCCCCGAGAGGCCTTTGCATTGTGGCAGGTGGCAAGCGAGGACTTCCAGCCCATCCTCGGGGTTCTGCTGGACG
Seq A exon
GTCAGTTGGAGGGGCAGCAGTGGGCCAGGTGATGCTCTGGGGGGTCCTCTCCCGCCTTCCGCGAAGGGGTCTCATGTGATTCTTGTCGCATCCCCCAG
Seq C2 exon
CCGGCAGGAAGTCGCTGACCTACTTCAACCGTGACCCCAGGGCCACCTTGCAGGAGGTCACCTTTGACCTGCCTGAAGTGAGGAGGATATTCTTTGGGAGTTTCCACAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000004582:ENSBTAT00000065814:22
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GAGCACACAGTCGTCTTCCTC
R:
CAAAGGTGACCTCCTGCAAGG
Band lengths:
181-279
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development