BtaINT0041331 @ bosTau6
Intron Retention
Gene
ENSBTAG00000004582 | COL20A1
Description
collagen, type XX, alpha 1 [Source:HGNC Symbol;Acc:HGNC:14670]
Coordinates
chr13:54751449-54751895:-
Coord C1 exon
chr13:54751752-54751895
Coord A exon
chr13:54751599-54751751
Coord C2 exon
chr13:54751449-54751598
Length
153 bp
Sequences
Splice sites
5' ss Seq
TGAGTAAGT
5' ss Score
8.82
3' ss Seq
CCCATCACATCTCTCTGCAGTCG
3' ss Score
8.06
Exon sequences
Seq C1 exon
GGGACCCAGAGCAGGAGGTGATGCTGACCACCAAGACCCCCAAGGCCACTGTGGGGGGCCTGAGCCCCTCCAAGGGGTACACCTTGCAGATCTTCGAGCTCACTGGCTCAGGGAACATCCTGCTGGCTCGCAGGGAGTTTGTGA
Seq A exon
GTAAGTGCCCTGGGCGTGCATGTGTGCAGAAGAGGCTGGGAGCCCATGGAGCCTGGATGGGCTTTTGTGGAAAGGGTTGCGTGGGCAGCCCCCAGGCCTCTATCCCCCGTGCCGGGCGGTGGGGTCCTGATATCCCATCACATCTCTCTGCAG
Seq C2 exon
TCGAGGATCTGAAGAGTAACTCTGTGAGCAGGAGCAGCCAGAGGCCACTGGGGGCAACCCTGGAGCCCACCCCTTCCCTTGTGGGGAGCCCAGACCTTGAGCCCCCAGGGGCCCTGGCCCCAAGCCAAGATCCACCCACGCTTGGTGGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000004582:ENSBTAT00000065814:4
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.374 A=NA C2=0.845
Domain overlap (PFAM):
C1:
PF0004116=fn3=PD(50.6=79.6)
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Rat
(rn6)
No conservation detected
Chicken
(galGal4)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GACCACCAAGACCCCCAAGG
R:
GTGGGTGGATCTTGGCTTGG
Band lengths:
258-411
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development