BtaINT0042462 @ bosTau6
Intron Retention
Gene
ENSBTAG00000015581 | COL9A3
Description
collagen, type IX, alpha 3 [Source:HGNC Symbol;Acc:HGNC:2219]
Coordinates
chr13:55024140-55024485:-
Coord C1 exon
chr13:55024453-55024485
Coord A exon
chr13:55024287-55024452
Coord C2 exon
chr13:55024140-55024286
Length
166 bp
Sequences
Splice sites
5' ss Seq
GAGGTGAGT
5' ss Score
10.03
3' ss Seq
CTGCTTCTGTTTCCCTCCAGTCT
3' ss Score
10.49
Exon sequences
Seq C1 exon
GGTCCCAGCGGCCCTGTTGGCCCCAAAGGAGAG
Seq A exon
GTGAGTGCCTGGCAGACACTGGCTCCCCGGCCCCCTTGGGGCCCCAGGCTGGCTCTGGGGCACTGATGGCCATGTGGGTCAGAAGTGGGGAAACTGCCAGCTCCGAGGGAGAAGCCCCTGCAGGTGGCTCGGCCATGACCCCCTCCCTGCTTCTGTTTCCCTCCAG
Seq C2 exon
TCTGGCAGTCGCGGGGAGCTGGGCCCTAAGGGCATCCAGGGCCCCAATGGCACCAGCGGCGTAGATGGCGTCCCTGGCCCCCCTGGCCCCGTGGGCCTCCAGGGCGTGCGAGGCGTGCCTGGCATCACTGGAAAACCTGGGGTCCCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000015581:ENSBTAT00000020699:27
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=1.000
Domain overlap (PFAM):
C1:
PF0139113=Collagen=FE(14.9=100),PF0139113=Collagen=PU(11.1=63.6)
A:
NA
C2:
PF0139113=Collagen=PD(9.0=12.2),PF0139113=Collagen=FE(76.2=100)
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:
CTGTTGGCCCCAAAGGAGAG
R:
CCCCAGGTTTTCCAGTGATGC
Band lengths:
162-328
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development