BtaINT0094013 @ 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
chr13:75471578-75471924:+
Coord C1 exon
chr13:75471578-75471728
Coord A exon
chr13:75471729-75471820
Coord C2 exon
chr13:75471821-75471924
Length
92 bp
Sequences
Splice sites
5' ss Seq
GAGGTGAGA
5' ss Score
7.66
3' ss Seq
TCCTCGGTGCCGTCCTGCAGGTT
3' ss Score
9.34
Exon sequences
Seq C1 exon
GGCGCCAAGTATGGGTGTACACCGGCGCGTCGTTGCTAGGCCCGAGGCGTCTGGACAAGTTGGGCCTGGGCCCGGAAGTGGCCCAGGTCACCGGGGCCCTCCCGCGCCCTGAGGGTAAGGTGCTGCTGTTCAGCGGGCAGAGCTTCTGGAG
Seq A exon
GTGAGATTCCCGGGGACCGCCAGCAGGGGGAGCCCGGGCGCCACCCGCCTGCCCGCCGGCTCAGCGCCTGTCTCCTCGGTGCCGTCCTGCAG
Seq C2 exon
GTTCGACGTGAAGACACAGAAGGTGGATCCCCAGAGCGTCACCCCCGTGGACCAGATGTTCCCCGGGGTGCCCATTAGCACGCACGACATCTTTCAGTACCAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000020676:ENSBTAT00000027556:11
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:
PF0004514=Hemopexin=PD(57.1=47.1),PF0004514=Hemopexin=PU(45.7=41.2)
A:
NA
C2:
PF0004514=Hemopexin=PD(52.2=66.7),PF0004514=Hemopexin=PU(20.0=22.2)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GAGGCGTCTGGACAAGTTGG
R:
GAACATCTGGTCCACGGGGG
Band lengths:
169-261
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development