BtaINT0094012 @ 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
chr13:75471004-75471728:+
Coord C1 exon
chr13:75471004-75471143
Coord A exon
chr13:75471144-75471577
Coord C2 exon
chr13:75471578-75471728
Length
434 bp
Sequences
Splice sites
5' ss Seq
CTGGTTAGT
5' ss Score
6.32
3' ss Seq
TGTGAGCCTCTCTTCGGCAGGGC
3' ss Score
6.08
Exon sequences
Seq C1 exon
GAAGTACTGGAGACTTTCTGAGGGAGGGGGCCGCCGGGTGCAGGGTCCCTTCCTTGTCAAGAGCAAGTGGCCTGCGCTGCCCCGCAAGCTGGACTCCGCCTTCGAGGATCCGCTCACCAAGAAGATTTTCTTCTTCTCTG
Seq A exon
GTTAGTTTTCGTCTTTCTCCCTCCCCTGTGCTGTGCTTGGTCGCTCAGTCGTGTCCGACTCTTTGCGACCCTGTGGACTGTAGCCCACCAGGTTCCTCTGTCCATGGGGATTCTCCAGGCAAGAAGACTGGAGTGGGTTGCCATTTCTTCTTTCTCCTGGGGATCTTCCCCACCCAGGGATCGAACTGGGTATCCCGCATTGCAGGCAGATTATTTACCGTCTGAGCCACCAGGGGAGCCCTGAACAAATTTAGCAGGGCTGAATTTCAGCCCTCCTCACAGCACCCTGGCACAGTCCTACCGAGGGGCTCTGCTCCTTGGGCACAGAGACTGCGGGCACTCCTGGACCGTGCCTGCGTTTTCCCTCTTGACATTCAAGGGGGGTGTGTACCCCACTCCCTGCCCCCAGACCGATGTGAGCCTCTCTTCGGCAG
Seq C2 exon
GGCGCCAAGTATGGGTGTACACCGGCGCGTCGTTGCTAGGCCCGAGGCGTCTGGACAAGTTGGGCCTGGGCCCGGAAGTGGCCCAGGTCACCGGGGCCCTCCCGCGCCCTGAGGGTAAGGTGCTGCTGTTCAGCGGGCAGAGCTTCTGGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000020676:ENSBTAT00000027556:10
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(62.2=58.3),PF0004514=Hemopexin=PU(40.5=35.4)
A:
NA
C2:
PF0004514=Hemopexin=PD(57.1=47.1),PF0004514=Hemopexin=PU(45.7=41.2)
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:
ACTGGAGACTTTCTGAGGGAGG
R:
CTCCAGAAGCTCTGCCCG
Band lengths:
286-720
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development