DreINT0096904 @ danRer10
Intron Retention
Gene
ENSDARG00000042816 | mmp9
Description
matrix metallopeptidase 9 [Source:ZFIN;Acc:ZDB-GENE-040426-2132]
Coordinates
chr8:24271621-24272095:+
Coord C1 exon
chr8:24271621-24271776
Coord A exon
chr8:24271777-24271890
Coord C2 exon
chr8:24271891-24272095
Length
114 bp
Sequences
Splice sites
5' ss Seq
ATGGTACAT
5' ss Score
4.52
3' ss Seq
ATTTAATTATGTGTTTTAAGGAC
3' ss Score
6.59
Exon sequences
Seq C1 exon
GATACAGTCTGTTTCTGGTGGCTGCTCATGAGTTTGGACATGCTCTTGGTTTGGATCACTCCAACATTAAAGATGCCCTGATGTATCCCATGTACAAATACGTGGAGGGTTTCCCCCTGCATCGTGACGATATTGATGGCATTCAGTATCTCTATG
Seq A exon
GTACATATCCACTGGTTTTTAAGATCACTATGCAATTTCTTATTCAAGATGAACTGATTCTGAAGCTCAATTCTGGTTTTATATCTGCATTTTTATTTAATTATGTGTTTTAAG
Seq C2 exon
GACCTAGAACTGGCCCTGAACCCACTGCTCCTCAACCACGGACCACCACTTCCTCTCCAGTTGTGCCAACGAAACCTTCTCCAAGTGACAAAACAACCACTGCTTCCACCACAACTCAGGTGGTCCCTTCAGACGATGCCTGCCAAATCAAGGAGTTTGACGCCATCACTGAAATCCAGAAGGAGCTTCACTTCTTCAAGGACGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000042816:ENSDART00000062845:8
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=0.609
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(37.2=23.2)
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:
GGCTGCTCATGAGTTTGGACA
R:
CCTGAGTTGTGGTGGAAGCAG
Band lengths:
257-371
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]