BtaINT0094011 @ 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
chr13:75466513-75467401:+
Coord C1 exon
chr13:75466513-75466656
Coord A exon
chr13:75466657-75467168
Coord C2 exon
chr13:75467169-75467401
Length
512 bp
Sequences
Splice sites
5' ss Seq
GAGGTAGGC
5' ss Score
8.99
3' ss Seq
CCCTGCCCTTCCTTCCACAGGAA
3' ss Score
13.93
Exon sequences
Seq C1 exon
CTCACCATGAGCCCCCTGCAGCCCTTGGTCCTGGCGCTCCTGGTGCTGGCTTGCTGCTCTGCTGTCCCCAGACGACGCCAGCCCACCGTTGTGGTCTTTCCAGGAGAACCACGAACCAACCTCACCAACAGGCAGCTGGCAGAG
Seq A exon
GTAGGCACACTCCCCCATCTAGAGTTGGGAAGGGCTGGCCGGGAGTCCCAGGAAGGGTGCGGGGTCTCAAACGAGATACTCTGGGGCTTGTTGTGGGGGGAGTGGTGATGGGCACCTCTGGAGGACAGAGCAGTGAGAACGGGCCCTGGGAGATTCTGGACAGGGACTGCTGGAAACAGGCTAGTGAGGGTTTCCTAGATGGGCACTGGGAAATGGATAAGGGGCACTGGGGGGTTCTGGAGTGGTGATGGGCTGAGGGCGAACAGGGGTAAACCCTAGGGGGCCCTGAAGTAGGCACTGCATGGGGGCATCCTGGAGTGGAACGGAGCTGAGGATGTCCACACGGAGGGGAGATTCTTGGGGCGGGCACAAGCCCTGGTATCCAGGGTACCGAGTACTGGATACAGTGTCTCGTTGCTAGTCTCCAAGAGCCGGGAGGGATGGAGTCCTTGCCCAGTAGGACAGAGAAAGGGCGTCGGGGCTCTGCCACGTCCCTGCCCTTCCTTCCACAG
Seq C2 exon
GAATACCTGTACCGCTATGGCTACACTCCTGGGGCAGAGCTGAGCGAGGACGGTCAGTCCCTGCAGCGAGCTCTGCTGCGCTTCCAGCGGCGCCTGTCCCTGCCCGAGACTGGCGAGCTGGACAGCACCACCCTGAACGCCATGCGAGCCCCGCGCTGCGGCGTCCCAGACGTGGGCAGATTCCAGACCTTTGAGGGCGAACTCAAGTGGCACCACCACAACATCACCTACTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000020676:ENSBTAT00000027556:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.109 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0147113=PG_binding_1=PU(14.0=17.4)
A:
NA
C2:
PF0147113=PG_binding_1=PD(82.5=60.3),PF0041319=Peptidase_M10=PU(2.7=11.5)
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:
CTCACCATGAGCCCCCTGC
R:
CGCCCTCAAAGGTCTGGAATC
Band lengths:
343-855
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development