BtaINT0041311 @ bosTau6
Intron Retention
Gene
ENSBTAG00000004582 | COL20A1
Description
collagen, type XX, alpha 1 [Source:HGNC Symbol;Acc:HGNC:14670]
Coordinates
chr13:54744459-54744836:-
Coord C1 exon
chr13:54744694-54744836
Coord A exon
chr13:54744592-54744693
Coord C2 exon
chr13:54744459-54744591
Length
102 bp
Sequences
Splice sites
5' ss Seq
GAGGTATGG
5' ss Score
8.98
3' ss Seq
CCAGTCCCTCTTCTCCACAGATT
3' ss Score
10.22
Exon sequences
Seq C1 exon
GGAAAGTCCCCAGCCCGAGCCAGCTGTCGGTGACAGAACTGCCTGGGGACGAAGTCCGGCTCGAGTGGGCGGCCGCGGCGGTGTCCGGCGTGCTTGTCTACCAGATCACGTGGATGCCCCTGGGAGAGGGGAAGGCCCGTGAG
Seq A exon
GTATGGGGGGAGTGGACCCTCCCCACCCCAGCTTCTCCCATGAGCCTGGCCCCCAGGGAAGGACACCTCCCCCAGGTGGACACCAGTCCCTCTTCTCCACAG
Seq C2 exon
ATTTCTGTCCCGGGGAACCTGGGCACGGCCATCCTGCCTGGCCTGGGGAGGCACTCAGAGTATGAGATCACCATCCTGGCCTACTACCGGGACGGGGCCCGCAGTGACCCTGTGTCCCTCCGTTACACCCCCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000004582:ENSBTAT00000065814:16
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.229 A=NA C2=0.119
Domain overlap (PFAM):
C1:
PF0004116=fn3=PU(53.7=91.7)
A:
NA
C2:
PF0004116=fn3=PD(43.9=80.0)
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:
GTCGGTGACAGAACTGCCTG
R:
TAACGGAGGGACACAGGGTC
Band lengths:
243-345
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development