BtaINT0041321 @ bosTau6
Intron Retention
Gene
ENSBTAG00000004582 | COL20A1
Description
collagen, type XX, alpha 1 [Source:HGNC Symbol;Acc:HGNC:14670]
Coordinates
chr13:54739446-54740119:-
Coord C1 exon
chr13:54740039-54740119
Coord A exon
chr13:54739533-54740038
Coord C2 exon
chr13:54739446-54739532
Length
506 bp
Sequences
Splice sites
5' ss Seq
TCGGTAGGT
5' ss Score
9.09
3' ss Seq
GGGGGTCTCCTTTCTCCCAGAAG
3' ss Score
6.12
Exon sequences
Seq C1 exon
AAGTTCCAGCTCCAGGTGCTACAGCTCGTGTGCAATGACTCGTGGGCAGAGGAGGACAGGTGCTGTGAGCTCCCAGCATCG
Seq A exon
GTAGGTGGCCAAGTGCCCACTGAGGGCAAGAGTCTGGGGGTAGACAGGCCATCCAGGTCATCCAGAAGAAGTGCGGACAGGCTTCCTGGAGGAGGTGACCCACAGGGCTGGAGCTGGAGCTCAGGGCAGCTGGATGGGTGTCCTGGAGACCCTGGGGCAAGGAAAGCTAGAGCAGGCCAGGCAGCCCCCAGCTCCAGGGTGGCTGCTGCCACGTACTCAGGGCCACTGCCCTTTTCTGTGGGCTCAGGCACAGGAAGGGGTCCTCACTGACTCCCCTGTGTGCCCACACTGGGCTTGGCCCTGCCGAGGGCTTGCAAGGGAACGAGAGATTGCATCCTGTCAGCAGGCCTGTACTGGGCAGCCAGGAAGGTGGCGGCCAGGACCAGGTCCCCACCCTTTACCCCTCGCCTCCCTGGACCCTGGAGTCAGTGCAGATACTGAGCTCTGGGGTTAAACAAGAGGCAAAGAGGGGGTGCATTTAATGGTGGGGGTCTCCTTTCTCCCAG
Seq C2 exon
AAGGAGGGAGAGTCCTGTCCTGCCTTCCCATCTGCCTGTGCATGTTCCTCACAGACCCCTGGGCCCCCAGGCCCCCAAGGACCTCCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000004582:ENSBTAT00000065814:25
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.037 A=NA C2=0.621
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0139113=Collagen=PU(18.6=37.9)
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:
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]
SPECIAL DATASETS
- Pre-implantation embryo development