BtaINT0093950 @ bosTau6
Intron Retention
Gene
ENSBTAG00000019267 | MMP2
Description
Bos taurus matrix metallopeptidase 2 (gelatinase A, 72kDa gelatinase, 72kDa type IV collagenase) (MMP2), mRNA. [Source:RefSeq mRNA;Acc:NM_174745]
Coordinates
chr18:23841001-23842524:+
Coord C1 exon
chr18:23841001-23841156
Coord A exon
chr18:23841157-23842388
Coord C2 exon
chr18:23842389-23842524
Length
1232 bp
Sequences
Splice sites
5' ss Seq
ATGGTAAGC
5' ss Score
9.26
3' ss Seq
GGTCGGGTGTCTTCCCCCAGGGG
3' ss Score
7.97
Exon sequences
Seq C1 exon
GGTACAGCCTGTTCCTGGTGGCAGCCCATGAGTTTGGCCATGCAATGGGGCTGGAGCACTCACAGGACCCTGGAGCCCTGATGGCGCCCATTTATACCTATACTAAGAACTTCCGCCTGTCCCATGATGACATCCAGGGCATCCAAGAACTCTATG
Seq A exon
GTAAGCCTCAGCTTGGGGTCCCTGGGGCAGGGATTTGGGGAGGTCGTGTCACTGGGGGTAGGGTGCCAGTGGGGGGAACCAGCCAGATCTGGGACTGCAGGAGACAAGGGCAGCAGTATTAACCTGGTCTGGGGATATTGGAGCATTACTCTAAGGCCTTTGGACAGCCCTTTCCTTTCCAAATAACACCAGTGTCTGAGCCTCACTTGGCTCCCCAGAGCCACGCCGCAAGGCAGGTGGGGCAGAAATGGGCTCTCCATTTTCTAGGTGAGTCAGCTGAGAAAGGTAACTTTCTGGCCTCAAGGTCAATGAGGTTTACGCATCCAAGTGAGGTTTAGAATCCAGGAGAAGTATTAATAGCTAAATACAGGGTAGAAATTCCCAGCACCTGGAATGACCTTAATGATACAGGAGTGCAAAACTTCTAGTTCTCCAAACAATTCTTTTATTTTAACGTGTAGTAGGATCAGTACAGCTAGTACCTGGAACCACTGATTTATGTATATTAATGCTTGCAATGAGGCTAGAGTTTACAAAGTGACTCCATTTTTTAAAATAAATCAACGTGTAATAGTACTGGCAGCACTTAGACAAGGCTGAAATCATGAAAATGGTTCTGGAGCGAAGAGGTGTGGGGAGCACAGGACTTGGGAAAGAACTGCAGTAGAGTGAGTGAGTGGCTCTGGGTTCGAGCGTCGCCTCTGCCACTCACCAGCTTCAAGGGATGGAGCCGGCCTTTACCTCTCTGGACTCAGTTTCCTCACCTCTAAACGGTGGCTGGTTACCCTCAGGAGTGAAGGAGGTGTCTGCCACACCCCCAGTGCTGGCCACACGGTCTCGCCTCTGACACTGACTCTCTTGTGGGCTCAGAAACCTGGGCTTTGAGTTTAAATCCTTGGGCAGGTCATATACAAAACTTGTCTGGGTCTCAGTTTCCTCATCTGTAAAATGGGAGTAAAGATGATGCCTACCTCTTAGGCATATAGAGAGGAATAATTAAGGGGATGTCGGGGAAGAACGTTCATACAAGGTGAAGGACCACAGGATTCTGGTTTCTGTTCAGTCTCCTTTCCAAGTCCAGGCCTCTTCCCTTGTCTTCCCTGGGCTGACACCGAGGCCAGAATGCTATTCTGATGGTCTTTAGCAGATTGGGTAGGCCGGTCTTGGGGCTCAGCCTGTGGGGGAGAACCCCTGGGGCTGGGGAGAGTCTGAGGTCGGGTGTCTTCCCCCAG
Seq C2 exon
GGGCCTCCCCTGACATTGATACTGGCACCGGCCCCACCCCAACCCTGGGCCCCGTCACTCCTGAGCTCTGCAAACAGGACATCGTCTTCGACGGCATCTCTCAGATCCGTGGGGAGATCTTCTTCTTCAAGGACCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000019267:ENSBTAT00000025657:8
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=0.283
Domain overlap (PFAM):
C1:
PF0041319=Peptidase_M10=FE(15.8=100)
A:
NA
C2:
PF0041319=Peptidase_M10=PD(0.1=0.0),PF0004514=Hemopexin=PU(36.4=34.8)
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:
GGTACAGCCTGTTCCTGGTGG
R:
TTGAAGAAGAAGATCTCCCCACG
Band lengths:
286-1518
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development