BtaINT0041334 @ bosTau6
Intron Retention
Gene
ENSBTAG00000004582 | COL20A1
Description
collagen, type XX, alpha 1 [Source:HGNC Symbol;Acc:HGNC:14670]
Coordinates
chr13:54748723-54749590:-
Coord C1 exon
chr13:54749471-54749590
Coord A exon
chr13:54748888-54749470
Coord C2 exon
chr13:54748723-54748887
Length
583 bp
Sequences
Splice sites
5' ss Seq
CAGGTCTGC
5' ss Score
5.61
3' ss Seq
TTGCTCTCACTGTGCCCAAGGCC
3' ss Score
4.06
Exon sequences
Seq C1 exon
GTCTGACTCAGTACAGTGGAGCCCCCCAGACCGAGTGGGACCTGAATGCCTTTGGCACCAAGGAGGAGGTGTTGAATGCTGTGCACAACCTCCACTACAGAGGAGGAAACACATTCACAG
Seq A exon
GTCTGCCCGGCCCCAGCCCCAGCCCCAGCCTCGGCCCCACCCTCGAGGTCCATTCAGGTCTTGTCCCGTGATTAGTCTCCCTTGCACCCACAGATAAGGAGAGGCATGCATGAACCACGCCCGAGTCCTGTGTTTTCATGCCTTTGCAGAGGGCCAGTCTGCCTCGTTCATCCATGGTGAATGTGGCAAGTCGGGCAGTACTGCTGAAAACAAGTTGCTCCTCTGGTCAGTAGAGGCTCCTGGGAAGGCCCACCAACAGCTTGGGGGAGCCCTGTTTTCAGCAGTCCTCCTCAGGGGAGAGGACTGCTGACCCAGGCAGACCACACACCCATGGCACAATTCCCTCCCTGATCCCCATTCACCCTGTGCACCCTGCAGCAGCAAGGTGTGGGGTGCTGGCCCCTGGGTCTCGGGTGCCTGTGAGGGAAGGAAGGGGGAATCCTTGCCCTCCAGGCACCCACAGTCTGAAGGGGCCAGGACTGCCCTGGTGGGCAGAGCAGATGGCCAGTGGCTGGTGGAGCCATCGCAGGTGGGCAGGAGAGTGTGTGGGGGCATGAGCACTCTTGCTCTCACTGTGCCCAAG
Seq C2 exon
GCCTGGCCCTGACCCACGTGCTGGAGCAGAACCTGAAGCCCAGAGCAGGTCTCCGTCCAGAGGCGGCCAAGCTGGTGATTCTGGTGACAGATGGCAAGTCCCAGGATGATGCCCACACTGCTGGCCACGTGCTCAAGGGTCTGGGTGTCGACATCTTTGCTGTGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000004582:ENSBTAT00000065814:7
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.081 A=NA C2=0.054
Domain overlap (PFAM):
C1:
PF0009223=VWA=FE(23.1=100)
A:
NA
C2:
PF0009223=VWA=FE(31.8=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Rat
(rn6)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TGACTCAGTACAGTGGAGCCC
R:
ACAGCAAAGATGTCGACACCC
Band lengths:
280-863
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development