BtaINT0093946 @ 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
chr18:23834517-23835038:+
Coord C1 exon
chr18:23834517-23834645
Coord A exon
chr18:23834646-23834864
Coord C2 exon
chr18:23834865-23835038
Length
219 bp
Sequences
Splice sites
5' ss Seq
AAGGTAAGA
5' ss Score
10.57
3' ss Seq
CACCCTGTGTGGCTCCTCAGTGG
3' ss Score
6.93
Exon sequences
Seq C1 exon
AGCATGGAGATGGGTACCCTTTTGATGGCAAAGACGGGCTCCTGGCTCATGCCTTCGCCCCGGGCCCTGGAGTTGGGGGAGATTCCCACTTTGATGACGATGAGCTGTGGACCCTGGGAGAAGGACAAG
Seq A exon
GTAAGAGTATGACCATCTACATGCCTGAGCCTCCTCGCCGATTTTCTGCATGCCTCCCTGTCACCTAGCAACGAAGACTGTGGCTTCCCTGGCAACTGTAGACCCCTCCATCTGCTCAGGTGGGAGGGGGAGGGAGGTCACACACCCCGATGAGTCACAATCCTGGTCTCCAAAGAAAGGCCTAGAGAGATTCACCCTCCACCCTGTGTGGCTCCTCAG
Seq C2 exon
TGGTCCGTGTGAAGTACGGGAATGCTGACGGGGAATATTGCAAGTTCCCCTTCCGGTTCAACGGCAAGGAGTACACCAGCTGCACAGACACAGGCCGCAGCGATGGCTTCCTCTGGTGTTCCACCACATACAACTTTGACAAGGACGGCAAGTATGGCTTCTGCCCCCATGAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000019267:ENSBTAT00000025657:4
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:
PF0041319=Peptidase_M10=FE(13.1=100)
A:
NA
C2:
PF0041319=Peptidase_M10=FE(17.6=100),PF0004014=fn2=WD(100=71.2)
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:
TTTTGATGGCAAAGACGGGCT
R:
CTTCATGGGGGCAGAAGC
Band lengths:
284-503
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development