BtaINT0094018 @ bosTau6
Intron Retention
Gene
ENSBTAG00000020676 | MMP9
Description
Bos taurus matrix metallopeptidase 9 (gelatinase B, 92kDa gelatinase, 92kDa type IV collagenase) (MMP9), mRNA. [Source:RefSeq mRNA;Acc:NM_174744]
Coordinates
chr13:75468420-75468975:+
Coord C1 exon
chr13:75468420-75468593
Coord A exon
chr13:75468594-75468801
Coord C2 exon
chr13:75468802-75468975
Length
208 bp
Sequences
Splice sites
5' ss Seq
AGAGTGAGT
5' ss Score
7.36
3' ss Seq
TAATCGTGTGGGCCTCCCAGGAC
3' ss Score
4.39
Exon sequences
Seq C1 exon
TGATCCCGACCTACTTCGGAAACGCGAAGGGCGCCGCCTGCCACTTCCCCTTCACCTTTGAGGGTCGCTCCTACTCCGCCTGCACCACGGACGGCCGTTCCGACGACATGCTCTGGTGCAGCACCACCGCCGACTACGACGCCGACCGCCAGTTCGGCTTCTGCCCCAGCGAGA
Seq A exon
GTGAGTGCCCACCCTCCCGAGGGTCCAGAGCGCTGGCTCTTAATCCCAGCTCTGCCACTGATGCCGAGGGTGGCCTGCGAACCCCTCTCCTGTTCTCTGGGCCCAGTTCCCTCATCTGTGAGACGAGGCGAGAAAGGGGAGGAGGACACAGGTGGCTCGTGGGTCAGTTAACTCGCGGCACCTTCAGTTAATCGTGTGGGCCTCCCAG
Seq C2 exon
GACTCTACACCCAGGACGGCAATGCGGACGGCAAGCCCTGCGTCTTCCCGTTCACCTTCCAGGGCCGCACCTACTCCGCCTGTACCTCCGATGGTCGCTCCGACGGCTACCGCTGGTGCGCCACCACCGCCAACTACGACCAGGACAAGCTCTACGGCTTCTGCCCGACCCGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000020676:ENSBTAT00000027556:5
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0041319=Peptidase_M10=FE(17.6=100),PF0004014=fn2=WD(100=71.2)
A:
NA
C2:
PF0041319=Peptidase_M10=FE(17.6=100),PF0004014=fn2=WD(100=71.2)
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:
TTCCCCTTCACCTTTGAGGGT
R:
AGAAGCCGTAGAGCTTGTCCT
Band lengths:
292-500
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development