DreINT0096894 @ danRer10
Intron Retention
Gene
ENSDARG00000042816 | mmp9
Description
matrix metallopeptidase 9 [Source:ZFIN;Acc:ZDB-GENE-040426-2132]
Coordinates
chr8:24260273-24261138:+
Coord C1 exon
chr8:24260273-24260509
Coord A exon
chr8:24260510-24260899
Coord C2 exon
chr8:24260900-24261138
Length
390 bp
Sequences
Splice sites
5' ss Seq
GATGTGAGT
5' ss Score
7.77
3' ss Seq
CCATAAATGTTTGTCTTCAGGAG
3' ss Score
8.1
Exon sequences
Seq C1 exon
GACACAGCAACACTGCTTCCACTTCATCTGATCTGATCTGAGCACTTGCAAGACAGTTTCTCCAGATTTCTTCTGAATTTACTTTTATATTTGCGACTCAAAATGAGACTTGGAGTCCTGGCGTTTCTGGTTCTGGGCACCTGCTCGTTGAGAGCCTGGTGTTTGCCACTCAAATCTGTGTTCGTGACGTTTCCTGGAGATGTGATCAAGAACATGACCAACACACAGCTAGCGGAT
Seq A exon
GTGAGTATGTCAGGTTTTAGGGATACACTTTAAGTGTAATTGTCTTCCAGGTTAACTATAAGTAAGTCTGCAACTACATATCAGCTGTCTTGTTATACTGTCGGTTTTAATAGTACAAGTTGACATGTACTTGCAAACTTACTTATAGTTAGTAGAACATCTGTTAAAGGACTATTAAAATAAAGAGTTACGAGATAGTAATAAAACTTCAAAGACGTTAAATTGCAAATTTAAGAGACTGTTTAAAAGCAGACCATTAAACTAAAGTAGAAGCAGTTTTAGTTTATGATTTGTTTGGGTTTCTCCTCTCGGTTCTCTACTTTTAAAGTGCAAATAACTGGATGTTATAGCTCCGCATGATTTGTTTTGTCCATAAATGTTTGTCTTCAG
Seq C2 exon
GAGTATCTGAAGCGTTACGGCTACATCGATGTCCTCCAGAGGAGCGGACTGCAGGCGGTCGTCTCCAATACTAAAGCTCTGAAGAAGCTCCAGCGGCAGCTCGGTTTGGAGGAGACCGGCTTGCTTGACCAGCCCACCGTTGATGCCATGAAGCAGCCCCGCTGTGGCGTGCCGGACATCCGCAACTACAAGACATTCGACGGAGACCTGAAGTGGGATCACACAGATGTCACATACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000042816:ENSDART00000062845:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0147113=PG_binding_1=PU(13.6=17.8)
A:
NA
C2:
PF0147113=PG_binding_1=PD(83.1=61.2),PF0041319=Peptidase_M10=PU(2.7=11.2)
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:
GAGTCCTGGCGTTTCTGGTTC
R:
TGATCCCACTTCAGGTCTCCG
Band lengths:
346-736
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]