BtaINT0041305 @ bosTau6
Intron Retention
Gene
ENSBTAG00000004582 | COL20A1
Description
collagen, type XX, alpha 1 [Source:HGNC Symbol;Acc:HGNC:14670]
Coordinates
chr13:54747108-54747667:-
Coord C1 exon
chr13:54747513-54747667
Coord A exon
chr13:54747238-54747512
Coord C2 exon
chr13:54747108-54747237
Length
275 bp
Sequences
Splice sites
5' ss Seq
GAGGTGAGC
5' ss Score
8.7
3' ss Seq
CCTCGCGGCTCCTATTCCAGGTG
3' ss Score
9.78
Exon sequences
Seq C1 exon
CTACACCGGCCCTGGATCCCCCTCCTGCTCCCACAAGGCTGGTCCTGACCCAAGTGACCTCCTCCAGCGTCCTCTTGTCCTGGAGCCCGGCCCCACAGCCGCCCCTCAAGTACCTGATTGTGTGGAGGCCTTCCAAGGGCGGCACCCCCAGGGAG
Seq A exon
GTGAGCACCGGCCCCCCAGCCCCGCCACCGCAGGCAGGGCTGGAGTAACGCCCACAGGTGATAAAATCAAGGTGAATGAGGAGCAGGTGCGGGAGGTTTATGCAACCACGGCCCCACGCACCCGTGGATGGCAGGGTTGTGCTCACGCCTGTGTGACAGGCTGATGGCCCAGACCTGCTCTGGGAACACAGCTGTGCAGGGAGTGAAGGCTGACCCAGCACCCCTTCCTGCTCCCCTGCACCCCACCGACCTGCTCCTCGCGGCTCCTATTCCAG
Seq C2 exon
GTGGTGGTGGAAGGGCCCACCTCGTCAGCACAGCTGCACAACCTGACCTCCAGCACCGAGTACCTGGTCTCTGTGTTCCCCCTCTACAAGGCTGGCGTCGGCGAGGGCCTGCAGGGCCTGGCGACCACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000004582:ENSBTAT00000065814:10
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.308 A=NA C2=0.386
Domain overlap (PFAM):
C1:
PF0004116=fn3=PU(53.8=82.7)
A:
NA
C2:
PF0004116=fn3=PD(43.8=79.5)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CTACACCGGCCCTGGATCC
R:
CGACGCCAGCCTTGTAGAG
Band lengths:
255-530
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development