BtaINT0042463 @ bosTau6
Intron Retention
Gene
ENSBTAG00000015581 | COL9A3
Description
collagen, type IX, alpha 3 [Source:HGNC Symbol;Acc:HGNC:2219]
Coordinates
chr13:55023927-55024286:-
Coord C1 exon
chr13:55024140-55024286
Coord A exon
chr13:55023982-55024139
Coord C2 exon
chr13:55023927-55023981
Length
158 bp
Sequences
Splice sites
5' ss Seq
CCGGTACGT
5' ss Score
10.49
3' ss Seq
GATTTGGGGGTGAATTTCAGGGG
3' ss Score
2.86
Exon sequences
Seq C1 exon
TCTGGCAGTCGCGGGGAGCTGGGCCCTAAGGGCATCCAGGGCCCCAATGGCACCAGCGGCGTAGATGGCGTCCCTGGCCCCCCTGGCCCCGTGGGCCTCCAGGGCGTGCGAGGCGTGCCTGGCATCACTGGAAAACCTGGGGTCCCG
Seq A exon
GTACGTGTCCCCTGGGAGCCAGTGCTCCTGCATGTTGGGCTCTTCCTGGATCTGGATCAAGTCCTTTCCAGACAATCAGGGTTCCTAGTGTTCGTGGGGGTGCCCCAAAGAGAAGTCAGTGGGCCCAATATGATGATGGATTTGGGGGTGAATTTCAG
Seq C2 exon
GGGAAAGAAGCCAGCGAGCAACACATCAGGGAGCTGTGCGGGGGGCTGGTCAGTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000015581:ENSBTAT00000020699:28
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=1.000 A=NA C2=0.974
Domain overlap (PFAM):
C1:
PF0139113=Collagen=PD(9.0=12.2),PF0139113=Collagen=FE(76.2=100)
A:
NA
C2:
PF0139113=Collagen=PD(7.9=26.3)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GGGAGCTGGGCCCTAAGG
R:
CAGCTCCCTGATGTGTTGCTC
Band lengths:
170-328
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development