RnoINT0093263 @ rn6
Intron Retention
Gene
ENSRNOG00000017539 | Mmp9
Description
matrix metallopeptidase 9 [Source:RGD Symbol;Acc:621320]
Coordinates
chr3:161416433-161417663:+
Coord C1 exon
chr3:161416433-161416588
Coord A exon
chr3:161416589-161417377
Coord C2 exon
chr3:161417378-161417663
Length
789 bp
Sequences
Splice sites
5' ss Seq
ATGGTGAGG
5' ss Score
7.61
3' ss Seq
ACCTAGTGTCTTGTTTTTAGGTC
3' ss Score
9.14
Exon sequences
Seq C1 exon
GGTACAGCCTGTTTCTGGTGGCAGCGCACGAGTTCGGCCATGCGCTGGGCTTAGATCATTCTTCAGTGCCGGAAGCGCTCATGTACCCCATGTATCACTACCACGAGGACTCCCCTCTGCATGAAGACGACATAAAAGGCATCCAGCATCTGTATG
Seq A exon
GTGAGGCTGGGGGACAGATGGCAGAGCAGAGGAGAGGGTGTGGCTCAGCTGTAGGAAGGGGGAGGGGAGAAATGGAACCTCGGAATCTATCTGGGTCAGGGCCTAGCAACTGCTTGGAGATGGCCCTCTAGGCCAGGGTTCAGAAGCCAGCCCAGGGCTGGGTGTGTAGCTTAGTGTTAGAGACATACTAAGTGCTGCAAAGCAGACACGAGGCCCTGGGTTTGATGCTCACCAAGAAGGGTCAGCCAAGCCACTTCATAGGGATTTGTATGGGTGTTTCGCCTGAATATGTGTACCGTGTATATGCAATGTCAGCAGAGGCCAGAAGAGGGCGTTAGATCGCTTACGTTAGAAAACTGGAGAACAAATTGCTGTGAGCGGATGGGTGTTGGGAAATGAACCCAGGTCCTCTGGAAGAGCAGCCAGTGGTCTTAACCATTGAGCCACATCTTCAGCCCCCAAGCTTTTAAAGGCATAGCCAGCCAGGCACGGTTGCACTTACGAAGCAGAGGCAGCTCCCAGCACTGTTTGACATGGTGGTGACCCAAAAGACTCTCTTCCTGCCTGACTTGGGGAAGGGAGGGAGATTCTGTCCGTTCTGTTCTGAGAACTCAGTCCATATCTTCACAGAGCTCAGTTCTGGATACTTAGGCTTGGTGTATGAGAAGAGGTTTGCTTGTAGCCTCTAGCTTCAATGGAAGCCTGAAGGCACCATTGCTGGGTGTGGTAGTAGGCTGGGGCTACAGAGAAATGGCGACTAGAGTGTCTTACCTAGTGTCTTGTTTTTAG
Seq C2 exon
GTCGTGGCTCTAAACCTGACCCAAGGCCTCCAGCCACCACCGCAGCTGAACCACAGCCGACAGCTCCTCCCACTATGTGTCCCACTGCACCTCCCATGGCCTATCCCACAGGGGGCCCCACAGTCGCCCCTACAGGCGCCCCCTCACCTGGCCCCACAGGTCCCCCTACTGCTGGTCCTTCTGAGGCCCCTACAGAGTCTTCGACTCCAGTAGACAATCCTTGCAATGTGGATGTTTTTGATGCCATTGCTGATATCCAGGGCGCTCTGCATTTCTTCAAGGACGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000017539:ENSRNOT00000023965:8
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.226 A=NA C2=0.781
Domain overlap (PFAM):
C1:
PF0041319=Peptidase_M10=FE(15.8=100)
A:
NA
C2:
PF0041319=Peptidase_M10=PD(0.1=0.0),PF048867=PT=WD(100=37.5),PF0004514=Hemopexin=PU(35.6=16.7)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GGTACAGCCTGTTTCTGGTGG
R:
CTCTGTAGGGGCCTCAGAAGG
Band lengths:
353-1142
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]