BtaINT0042446 @ bosTau6
Intron Retention
Gene
ENSBTAG00000015581 | COL9A3
Description
collagen, type IX, alpha 3 [Source:HGNC Symbol;Acc:HGNC:2219]
Coordinates
chr13:55039683-55040430:-
Coord C1 exon
chr13:55040353-55040430
Coord A exon
chr13:55039752-55040352
Coord C2 exon
chr13:55039683-55039751
Length
601 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGC
5' ss Score
9.6
3' ss Seq
ATGATGTTTCTCCATTTCAGAAA
3' ss Score
10.34
Exon sequences
Seq C1 exon
ATGGCCGGAGCCCCCACCCTGGCCCTGCTGCTGTTGGGGCAGCTGCTGGCTGCCACCGTAATCTTGACTGAGGCACAG
Seq A exon
GTGAGCATGGGACCCGGGGCGCATGGGGCTTGCCTTTGAATGCAGCTAGGGTGGGGGTCCATGGCTCTGTGGTCACCTGTTGAGCAGCGCAGCCAGGGAATAAGCTCCCCACTTGCCCCCTGTAGCCAGTCTCCCTGAATCAGCGAGGGAGCCAGGAATTCCGGGGCACTTGGAGATGGCGGGCACAGTCTTGTCACTGCAAAGTTTCTGCACCACCTGGGCACAGGCTCGCCCTTGCCCGGGTGAGCCCCCATAGACACGGGGATACCCTGGGATTGAGTTCAGGGACTGCTCCGTCCTCAACCCAGCGGGTGTGGTGCCAGAGCTGCATCTCCACCAGAGACACACAATGTGGCCTTTGTTCCTCGTGGGCCTCGGACGTGGCCCCTCTTGGCCCAGCAAGGTGGCAGGGGACACTGCAACAGCCCGGGGGTCTGAAGGAGAATGGGGGAAGGGGCGGTGCGGACCCCTGCACAGGTCCGAGCTCTTCTCCGGACTGGGAGGAGGGGGTGCTCTGTCAGGCTAACCCCAGGGCCAACCAGGGGGACCCGCAGTGGGAGAGCATGGGGTGCTGCCACCTGATGATGTTTCTCCATTTCAG
Seq C2 exon
AAAGTGGGACCTCGAGGCCCCCCCGGTCCCCAAGGGCCACCTGGGAAGCCAGGAAAGGATGGCATTGAT
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000015581:ENSBTAT00000020699:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.308 A=NA C2=1.000
Domain overlap (PFAM):
C1:
PF0139113=Collagen=PU(1.6=3.8)
A:
NA
C2:
PF0139113=Collagen=FE(36.1=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Zebrafish
(danRer10)
No conservation detected
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