BtaINT0041319 @ bosTau6
Intron Retention
Gene
ENSBTAG00000004582 | COL20A1
Description
collagen, type XX, alpha 1 [Source:HGNC Symbol;Acc:HGNC:14670]
Coordinates
chr13:54740209-54740893:-
Coord C1 exon
chr13:54740784-54740893
Coord A exon
chr13:54740368-54740783
Coord C2 exon
chr13:54740209-54740367
Length
416 bp
Sequences
Splice sites
5' ss Seq
AAGGTACTG
5' ss Score
8.56
3' ss Seq
AACCTCCTGCTGTCTCCCAGGTG
3' ss Score
9.2
Exon sequences
Seq C1 exon
CCGGCAGGAAGTCGCTGACCTACTTCAACCGTGACCCCAGGGCCACCTTGCAGGAGGTCACCTTTGACCTGCCTGAAGTGAGGAGGATATTCTTTGGGAGTTTCCACAAG
Seq A exon
GTACTGGCAAGTCCTGGAAGGACCACCGCTCGTGCCTTCCTGCCTGATACCCTCGGTGCTCCCAGGTTCTGGGACAGACCCCCACTGGGCTCTGCAGGACACAGGCTGCCCTGTCACCATGGCACCCCCCAGAATGCAGGAACTTTGCTCTGCCCTGGATGCCCCCACCCTGATCTGGGTCAAAGAGCATCCAGCCCTTGCTCCTGGTCCCGCAGCCCCTGGGAGGGGCTGTGGGGGTGTCATTGTACAGAACAAAACTGAGGCCCTGTGAGGGGTTTCAGGAGATGTGGGGTGGTCAGGACCCAGACACCAGCCCCGGGAACGGTCCCTGCCCCTCCCTGCTCCGGGCCTGGCCCTTGGACATGGAGGGAGCCCATCCTGGCTGGGGCCCCGGGGAACCTCCTGCTGTCTCCCAG
Seq C2 exon
GTGCATGTGGCCGTGGGCCGAGCCAGGGTCAGGCTCTACGTGGACTGCCGGAAGGTGGCCGAGAGGCCCATCGGGGAGGCCGGCGGCCTGCCTGCTGCCGGCTTCGTCATGCTGGGCAGGTTGGCCAAAGCCCGGGGCCCCCGGAGCAGCTCCGCCTCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000004582:ENSBTAT00000065814:23
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.013
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GCAGGAAGTCGCTGACCTACT
R:
CCAACCTGCCCAGCATGAC
Band lengths:
231-647
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development