BtaINT0041329 @ bosTau6
Intron Retention
Gene
ENSBTAG00000004582 | COL20A1
Description
collagen, type XX, alpha 1 [Source:HGNC Symbol;Acc:HGNC:14670]
Coordinates
chr13:54734901-54735092:-
Coord C1 exon
chr13:54735057-54735092
Coord A exon
chr13:54734950-54735056
Coord C2 exon
chr13:54734901-54734949
Length
107 bp
Sequences
Splice sites
5' ss Seq
AAGGTGAGT
5' ss Score
10.47
3' ss Seq
TGGCCTGTCCTCCCTTGCAGGGA
3' ss Score
12.32
Exon sequences
Seq C1 exon
GGACTGCCGGGGCCCAAGGGGGAGCGAGGAGAGAAG
Seq A exon
GTGAGTGTGCAGAGTCTGGGGCCCGGGCCGACCCTGGGGGAGCACGGGGAGGCACTGACCCCCACACTGCCTGAGCCGTCAGCCACGTGGCCTGTCCTCCCTTGCAG
Seq C2 exon
GGAGAGCCACAGTCCCTGGCCACCATCTACCAGCTCGTGGGCCAGGCTT
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000004582:ENSBTAT00000065814:32
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=1.000 A=NA C2=0.732
Domain overlap (PFAM):
C1:
PF0139113=Collagen=FE(18.6=100)
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:
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