BtaINT0094021 @ 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
chr13:75469679-75470881:+
Coord C1 exon
chr13:75469679-75469834
Coord A exon
chr13:75469835-75470586
Coord C2 exon
chr13:75470587-75470881
Length
752 bp
Sequences
Splice sites
5' ss Seq
ATGGTGAGG
5' ss Score
7.61
3' ss Seq
TACGCGGTATCTTTTTTCAGGTC
3' ss Score
9.53
Exon sequences
Seq C1 exon
GATACAGCCTGTTCCTTGTGGCCGCACACGAGTTTGGCCACGCGCTGGGCTTAGATCACACCTCCGTGCCAGAGGCGCTCATGTACCCCATGTACAGATTCACAGAGGAGCACCCCCTGCATAGGGACGATGTTCAGGGCATCCAGCATCTGTATG
Seq A exon
GTGAGGGCGTGGGGCAGGGATAGAGGGAGGAGAGGGAAGGGCTAGGTTCTCCCGGCTCAGAACACCCCGAGAATAGGGAGGAGGGGAGAGTTAGGACTCTGATATCTATCTTTGAGAGCCCTTGAGGCTGGTGGGTACAACTGCTGCCAGGTCAGGACTTGGAGATGGCGATAAAGAGCCCCGACTCTAGAGTGAGACGGACATAGGTTCAAAAGCCGGTCCAGCCACTATCCGGCTAGATGACGTTGGATAGGTTACTTCACCCCTCAACTTCCTTATCTGTAAAGTGGGGCTAACACCTGCCTCATGGGGTTGTTAGGAGGCTTAAGTGAGTTAGAATAATGCCTGGAATATAGCAAGCACCATATAAATGTTTGATAGTTTTATTATTATCATCACTTATTATCATTAGTATGTTTCCGCATCAAAAAAATGAAAATATTAAAGAATCTGCTCCCTAGTTTTTTCTTTTTCCCCCTTCTGAAGATCAAAGGAGCTAATGTGCGTTTATAAAGCTCCCAGCACTGTTTGGCACCCAGTTTGAGAGCTCAAAAGAGGCTTCTCTCCCACCAGCCTGGGGGTGGGGGTGAGTGTGTGAAAGGAAGCTGCCAGCCCGGGGTTGGGGGAAGGCAGGATCCAACATTTGAAGTGGGGAGAGCGCCAGGGACCTCCAGGTAGGCACCAGGGAGCAGATACTCCAAAGGCACAGAGATGCAAGAACAGCGATTGCCTTACGCGGTATCTTTTTTCAG
Seq C2 exon
GTCCTCGCCCTGAGCCTGAACCACGGCCTCCGACCACTACCACCACTACCATCACCGAACCCCAGCCCACCGCTCCCCCCACGGTCTGCGTCACGGGGCCTCCCACCGCCCGCCCCTCAGAGGGTCCCACTACTGGCCCCACAGGGCCCCCGGCAGCTGGCCCCACGGGTCCTCCCACGGCTGGCCCTTCTGCGGCCCCGACGGAGTCCCCGGATCCAGCGGAGGACGTCTGCAACGTGGACATCTTCGACGCCATCGCGGAGATTAGGAACCGCTTGCATTTCTTCAAGGCTGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000020676:ENSBTAT00000027556:8
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.321 A=NA C2=0.788
Domain overlap (PFAM):
C1:
PF0041319=Peptidase_M10=FE(15.8=100)
A:
NA
C2:
PF0041319=Peptidase_M10=PD(0.1=0.0),PF048867=PT=WD(100=36.4),PF0004514=Hemopexin=PU(35.6=16.2)
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:
GCTTAGATCACACCTCCGTGC
R:
CGAAGATGTCCACGTTGCAGA
Band lengths:
357-1109
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development