BtaINT0042459 @ bosTau6
Intron Retention
Gene
ENSBTAG00000015581 | COL9A3
Description
collagen, type IX, alpha 3 [Source:HGNC Symbol;Acc:HGNC:2219]
Coordinates
chr13:55026205-55026633:-
Coord C1 exon
chr13:55026562-55026633
Coord A exon
chr13:55026241-55026561
Coord C2 exon
chr13:55026205-55026240
Length
321 bp
Sequences
Splice sites
5' ss Seq
CGGGTAAGT
5' ss Score
10.75
3' ss Seq
CATCACCCCTTTCTGACCAGGGC
3' ss Score
7.88
Exon sequences
Seq C1 exon
GGCCGGAAGGGCAGCATAGGAGACCCCGGCCTGCCGGGCCCCCAAGGCCTCCGAGGTGGTGTGGGCGACCGG
Seq A exon
GTAAGTGCTGTCCCTGCAGGAATCCCTGCACCCCCACGCCCCTCATCCCACCTCCCACAGTTCCACAACACACTCAAAGGCAGTGTTGGTGCCCAGTAGTCAGCACTGGGGGGTCCCCATTGTCCCTGAGACTTGGGGGCTGGGGCCATCAGGGAGGAGGCTAGGGGCAAGCTCCCAGCACGCTCAGGGGCCAAGATGCCAAGTGTCCGGGAGGAGCCCATGTGTGCCGAGCTGGTCCTGGCACCCCAGTGGGGGAAGGGCACTGGCCCCCTCCCCAACCCCGCTGTGATCCTCTAACGCTCATCACCCCTTTCTGACCAG
Seq C2 exon
GGCCCGGGAGGAGCTGCCGGCCCCAAGGGCGACCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000015581:ENSBTAT00000020699:24
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(30.3=100),PF0139113=Collagen=PU(31.3=87.5)
A:
NA
C2:
PF0139113=Collagen=PD(0.1=0.0),PF0139113=Collagen=FE(16.4=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:
No suggested primer sequences
R:
No suggested primer sequences
Band lengths:
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development