BtaINT0041330 @ bosTau6
Intron Retention
Gene
ENSBTAG00000004582 | COL20A1
Description
collagen, type XX, alpha 1 [Source:HGNC Symbol;Acc:HGNC:14670]
Coordinates
chr13:54734522-54734949:-
Coord C1 exon
chr13:54734901-54734949
Coord A exon
chr13:54734701-54734900
Coord C2 exon
chr13:54734522-54734700
Length
200 bp
Sequences
Splice sites
5' ss Seq
CTTGCGAGT
5' ss Score
-0.6
3' ss Seq
CATCTTCCCCCGCCCCCCAGCGC
3' ss Score
8.99
Exon sequences
Seq C1 exon
GGAGAGCCACAGTCCCTGGCCACCATCTACCAGCTCGTGGGCCAGGCTT
Seq A exon
GCGAGTCCGCCATCCAGAGTGAGTGGCCTTGCCTCCTGTGGTGCCCAGTGCCTCTGTCTTCACACTGGAGGGAAGGGAGCCCCGTGCCGGGTCATTGGTGCCCCAGCCTTGAGCAGTTCTCCTGGGCCGCTGCCTCCGGGCAAGGCAGGGAGCAAGGGAGGGTCTCCCAACCCCCACTGACATCTTCCCCCGCCCCCCAG
Seq C2 exon
CGCACGTGTTGAAGCTCCATGCCTGCACCCACGAGAGCACCCGGCCCCCCATGCCCATCTTGGAAGCCCCCAGGGCCCTTGGCACAAGCAACAAGGCCCGGCTCCCTGGAGAAGGGGGGCATGGTGGCCCCCACCCTGGGGACAGAGGTACTGGGGGAGGGGTCTTCTCCAGTCCTGGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000004582:ENSBTAT00000065814:33
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.732 A=NA C2=0.985
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Human
(hg38)
No conservation detected
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:
GGAGAGCCACAGTCCCTGG
R:
CAGGACTGGAGAAGACCCCTC
Band lengths:
226-426
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development