DreINT0096836 @ danRer10
Intron Retention
Gene
ENSDARG00000017676 | mmp2
Description
matrix metallopeptidase 2 [Source:ZFIN;Acc:ZDB-GENE-030131-9123]
Coordinates
chr7:35150224-35151005:-
Coord C1 exon
chr7:35150850-35151005
Coord A exon
chr7:35150351-35150849
Coord C2 exon
chr7:35150224-35150350
Length
499 bp
Sequences
Splice sites
5' ss Seq
ATGGTAAGT
5' ss Score
11.01
3' ss Seq
CTCTTCTTTTCTCTGTACAGGAG
3' ss Score
10.71
Exon sequences
Seq C1 exon
GTTACAGTCTATTCCTTGTGGCGGCCCATGAGTTCGGCCATGCCCTGGGTTTAGAGCATTCTGATGACCCCGGAGCTCTCATGGCTCCTATCTACACATTCACCAAAACCTTAAGACTGTCTGATGATGATGTTAAAGGCATCCAGGAGCTCTATG
Seq A exon
GTAAGTGTGACATGAAGATGATTTATATCTATGGAAATCATTTGTTTCTCTTGATTTAAAACACTGTACATAGTAAATAATTACATAGCTATGTTTTAAGTAAATCCATTTTCCCCCTGCAAAGTACTGATTTTTTTTCTACATTTCAATTAGAAATGCTAATGCTTGGAGCAAAAAAATGCCAAATAGTCAAAACAAAAAATATGCCATAATTTTAAATATGTTTATATTGACTTTTAGACACAATACCAATGATTAAAATGCTGTTTTCTGCAAAGAAAAAAAGAGAAATGCTCATAATATTTGTATTTTAAATCAGAAAAAGAAATGCTATCAGACTGTTATTAAAAACAACAAATTCCTAGAAAATTTACAGAAACTGAGAGCTTTCAAGTGGTCATTTAAATGTCCCATTCAGTATTGATTAATTCTGATGTTGCATTGATTATAATCATATTTAAAATTCTTTGACTTCTTTACTCTTCTTTTCTCTGTACAG
Seq C2 exon
GAGAACCAACAGACAAGCCATTGCCCACTCACACCCCACCAGTCACACCAATGGATGTATGTAATGAAAACATCATATTTGATGCTGTAGCCCAGATCAGAGGAGAGATCTTCTTCTTTAAGGACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000017676:ENSDART00000026712:8
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.057 A=NA C2=0.349
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=37.2)
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:
CAGTCTATTCCTTGTGGCGGC
R:
TGTCCTTAAAGAAGAAGATCTCTCCT
Band lengths:
278-777
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]