DreINT0096900 @ danRer10
Intron Retention
Gene
ENSDARG00000042816 | mmp9
Description
matrix metallopeptidase 9 [Source:ZFIN;Acc:ZDB-GENE-040426-2132]
Coordinates
chr8:24269885-24270694:+
Coord C1 exon
chr8:24269885-24270013
Coord A exon
chr8:24270014-24270520
Coord C2 exon
chr8:24270521-24270694
Length
507 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGT
5' ss Score
10.67
3' ss Seq
CAATAATATTCCTCCTTCAGCCA
3' ss Score
4.77
Exon sequences
Seq C1 exon
ATCACGGTGATCCCTACCCCTTTGATGGAAAAGATGGGCTGCTGGCTCACGCTTATCCTCCAGGTGAAGGCACACAGGGAGACGCTCATTTTGATGACGATGAATACTGGACCCTTGGCTCTGGACCAG
Seq A exon
GTGAGTGTCGTTTTAACTCAAGTAGCTTTGATAAATAGGTTAAGTGGTTTAAAACATAATTTAGCATCGCTCTTTATTATAACAACTGCATAGTGTGCATAGAGGAGCAATAGCTCCCTCTGCAGTTCTGAATGAGTAGTGACGGTTACAAACTTTTTTCTTTCAAAATTGTAATTAAAACAATGATTATTATATATATTTATTTTAAAGTAAAATACTATTTAAGATTTCTTTTTTAATCTTCCATGTTTATTCTTATTGTTTGTGTTTATTAGCAACTTCTGAGTAAAAATATTTCTTCACCATTTTGTTTTTCAATTTGAGATAGCATTTTAACATGTCCTTTGCAACAATAATAATACAAATTTTCATTTTATAAACGTGTTGTTTTTGCAATATTGGATGCAATCTAAAATATATATATACATCTCAGGAATACAAGAGGCGACCATAATGTTTCTATATATTACATTATAGTAGATATTGACAATAATATTCCTCCTTCAG
Seq C2 exon
CCATTCAAACCCGCTACGGTAATGCTGAGGGTGCAATGTGTCACTTCCCCTTCCTGTTTGAGGGAACATCCTACTCCACCTGCACCACTGAGGGCCGCACAGATGGCCTTCCCTGGTGCTCAACCACCGCAGACTATGACAAGGACAAGAAGTTTGGCTTCTGTCCCAGTGAGC
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000042816:ENSDART00000062845:4
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.114 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:
CACGGTGATCCCTACCCCTTT
R:
AGCCAAACTTCTTGTCCTTGTCA
Band lengths:
286-793
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]