BtaINT0093941 @ 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
chr18:23846749-23848522:+
Coord C1 exon
chr18:23846749-23846885
Coord A exon
chr18:23846886-23848362
Coord C2 exon
chr18:23848363-23848522
Length
1477 bp
Sequences
Splice sites
5' ss Seq
CAGGTCTGT
5' ss Score
6.84
3' ss Seq
ACCCTCTGCTTCTACCCAAGGGA
3' ss Score
5.58
Exon sequences
Seq C1 exon
ATTCATCTGGCGAACAGTGACACCACGTGACAAGCCCACAGGGCCCCTGCTGGTAGCCACATTCTGGCCTGAGCTGCCGGAAAAGATCGATGCTGTGTACGAAGACCCACAGGAGGAGAAGGCTGTGTTCTTTGCAG
Seq A exon
GTCTGTGGGAGGGGACCTTCTTGGCCCTCAGCTCCAGGGGGCGCTGTACCGAGATTCCTGTACGCTGGTGGGTGCTCCCCTTAGTTACAGATCCACTCTTTCAACCATCATCTGGGAGATTGGTTAGACATCCAGCATCAACCAGCACTGGCTCACAGAATGAACATTTCAGTAACCTTTTACTCACTTTGCAATCTTTTTGATTCCTTTTCCAAAGGAAAATGACACTTCAGTGCTACTGCCTTTAATACCTTCCTAATGCTAGTGCCTTCGGCAGATGACAGTTTTAGTTAGAATTTTTTAAACACTGATTTGTTTTTATTTTTAATGTTTACACTTATTTCTATAGACTTCAAAGTGAATTCCTTGAAAGCAGAATGTTGAGTTAAGTAATAGTACAAGGAGACTCTTGTTGTTTAGTTGGTAAGTTCTATCTGACTCTTTCCAACCCCATGGACTGTAGCCTACCAGGCTTCTCTGTCTGTGGGATTTCCCAAGCAAGAGTGGAGTGCCGTTTCCTTCTCTGGGGGATCTTCCCAACCCAGGGATCAAATCTGCGTCTCCTGCATTGCATTGGCAGGCATATTCTTTACTACTGAGCTACCAGGAAGGCCCATGAGGAGTCTCTATAAGTGGTAAAAATCATTGAGGTAGGGTCATATGGGCTTCCCAGGTGGCTCAGTGGTAAAGAATCCACCTGCCAGTTCAGGAGACACAGGTTTAATCCCTGGGTCGAGAAGATCCCCTGGAGAAAAATGGCAACCCACTCCAGTATTTTTGCTGGGAAATCCCATGGACAGATCAGCTTGGCGGGCTGCAGTCCATGAGGTCACAAAAGAGTTGAATGTGACTTAGCAACTGAACAACAGCAGCAGGGCCACCTGGGTAACATCTGGGAAACCTTGCTCCTTTCCTCTTTATTCGAGCGCCTCCCATGTCCCCAGGGCTGCAACCCTTGCTCTCAGGGAGCTCATGAGCCAGGAGGGGAGACAGAAAAACAGGCTGTTAGGAGGGGATTCAGGAAGAGCTGTGGCGGTTAGGGGGGTGAAGGCTGAGATGGGGACACAGGGACAGCTTCCTTGACGCTGAAGGCTCAGACAGCGCTGTGGGTGCATGCTCACCGGTGGACCCCCCAGCTCCTCCATCCCAGAGTGACCAGGGCAGCTGCTGGCTCACAGGGGACCTGGGTGCAAATTAGAAAAAGGTGCCTCTTCACGGCAGTTGTGGCACTTAGAATCTCTGACTTGGTGAATGAAGCCAGGGTGGGAATCATTCCTGCTCACCTTCTTGGCCAGGGACCTTCCATAACCAATTTACGAAGCCTTACATGGAGGCCCCGATTCTGGGCACTGAATCCAGAAGTGAGCAGAACTCATGTACCCGTTGAGAAAGGCCACAGTGGGGTCGCTGGCAGATTGGTGGTGGGAGGAACAGCCTTGAGCACTTGCCACCAACGCACCCTCTGCTTCTACCCAAG
Seq C2 exon
GGAACGAATACTGGGTCTATTCAGCCAGTACCCTGGAGCGAGGGTACCCCAAGCCACTGACCAGCCTGGGGCTCCCCCCTGGTGTCCAGAAGGTGGATGCTGCCTTTAACTGGAGCAAGAACAAGAAGACGTACATCTTCGCCGGAGACAAATTCTGGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000019267:ENSBTAT00000025657:10
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(61.4=57.4),PF0004514=Hemopexin=PU(38.6=36.2)
A:
NA
C2:
PF0004514=Hemopexin=PD(59.1=48.1),PF0004514=Hemopexin=PU(45.8=40.7)
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:
CTGGCGAACAGTGACACCAC
R:
CCAGAATTTGTCTCCGGCGAA
Band lengths:
289-1766
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development