BtaINT0042464 @ bosTau6
Intron Retention
Gene
ENSBTAG00000015581 | COL9A3
Description
collagen, type IX, alpha 3 [Source:HGNC Symbol;Acc:HGNC:2219]
Coordinates
chr13:55023273-55023981:-
Coord C1 exon
chr13:55023927-55023981
Coord A exon
chr13:55023459-55023926
Coord C2 exon
chr13:55023273-55023458
Length
468 bp
Sequences
Splice sites
5' ss Seq
GTGGTGAGT
5' ss Score
8.95
3' ss Seq
GCCTGATCTTTGTTTTCCAAAAG
3' ss Score
-0.55
Exon sequences
Seq C1 exon
GGGAAAGAAGCCAGCGAGCAACACATCAGGGAGCTGTGCGGGGGGCTGGTCAGTG
Seq A exon
GTGAGTGTCCTTCCTCCCTCCNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNCCACCCTCCATCACCTTCCAGCCAAGCCCACTGCTGGCGTCCCTGGGGTCTGCACTGGGTGGGCTCCTTCCCCTCAGCATTTCTTAGGCCTGTGATTTGCTCCTCGGCATTTCTCAGGGACAGCATACTGACACCATTTCTCACAGACCCAAAGCAGTTACAGCCCTTCGCAGTCAATGAACAAGCTGTCTTTGAAGAGCGGTATGCTCACACTTCACGTAACACACTTCTGATGAATACACGCCTGATCTTTGTTTTCCAA
Seq C2 exon
AAGAGCAAATCGCGCAACTGGCCGCGCACCTGAGGAAGCCCCTAGCACCAGGCTCCATCGGGCGACCGGGTCCTGCTGGCCCCCCGGGCCCCCCGGGCCCCCCAGGCTCCATTGGTCACCCCGGGGCTCGAGGGCCCCCTGGATACCGAGGTCCCACAGGAGAGCTTGGAGACCCTGGACCCAGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000015581:ENSBTAT00000020699:29
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.974 A=NA C2=0.992
Domain overlap (PFAM):
C1:
PF0139113=Collagen=PD(7.9=26.3)
A:
NA
C2:
PF0139113=Collagen=PU(75.8=74.6)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Rat
(rn6)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GAAAGAAGCCAGCGAGCAACA
R:
TCTGGGTCCAGGGTCTCCAAG
Band lengths:
238-706
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development