RnoINT0093253 @ rn6
Intron Retention
Gene
ENSRNOG00000017539 | Mmp9
Description
matrix metallopeptidase 9 [Source:RGD Symbol;Acc:621320]
Coordinates
chr3:161413298-161414224:+
Coord C1 exon
chr3:161413298-161413550
Coord A exon
chr3:161413551-161413991
Coord C2 exon
chr3:161413992-161414224
Length
441 bp
Sequences
Splice sites
5' ss Seq
GAGGTAGAC
5' ss Score
5.41
3' ss Seq
GCCCCTTTCTCCACCCACAGGAT
3' ss Score
11.74
Exon sequences
Seq C1 exon
ACACCCTGAGTCAGCGTAAGCCTGGAGGGAGGGGCGGGGACACTGATTCAGTTTTCGTGCCTCTTTAAAACCTCCGCAAATTCTGCTTCACCCAGAAGCTTCGGTTCTCACCATGAACCCCTGGCAGCCCCTGCTCCTGGTGCTCCTGGCTCTAGGCTACAGCTTTGCTGCCCCTCACCAGCGCCAGCCGACTTATGTGGTCTTCCCCCGAGACCTGAAAACCTCCAACCTCACGGACACACAGCTGGCAGAG
Seq A exon
GTAGACAGATGGCTCAGTGAAAGTTGGGAAGGGCTGGCCAGGAAGATGTCCACTATCCCAAGGAAGGGGGCCTCAAGTGCTTTCTGGATTTGGGAGTGATGGGCATGTCTAGAGAAAAAGAGGTGCCAGGGTTAGGCAGCAGGGGTAGGTGGTCTGGAGGCTCTGGGCAGATTGGGGTTTACTGGAGGGATGGAATGGGGAGGGCTTCGAAGGGCTGTGACATAGGCCGAGGTTGGCAGTGAACAGTTAAATTGTGGGGGGCTGTGTGGTAGGCATGGCTTATGTCATCTGAAGTGGGGAGGAGTGATGCGATCCTCGGATAGGGGAATTCTAGCTGTGCAGGAAGAACTGGTGTCCTGGGCTTAGAGTCCCTAAGTGTGTGTTCCCAGAAGGGAAGGTGCCAGAACTCTGAGATATCTTTGCCCCTTTCTCCACCCACAG
Seq C2 exon
GATTACCTGTACCGCTATGGTTACACTCGGGCAGCCCAGATGATGGGAGAGAAGCAGTCCCTGCGGCCCGCTTTGCTGATGCTTCAGAAGCAGCTGTCCCTGCCCCAGACTGGTGAGCTGGACAGCGAGACACTAAAGGCCATTCGTTCACCGCGCTGTGGTGTCCCAGACGTGGGCAAATTCCAAACCTTCGAAGGCGACCTCAAGTGGCACCATCATAACATCACCTATTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000017539:ENSRNOT00000023965:1
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(14.0=17.0)
A:
NA
C2:
PF0147113=PG_binding_1=PD(82.5=60.3),PF0041319=Peptidase_M10=PU(2.7=11.5)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CCAGAAGCTTCGGTTCTCACC
R:
AGGTTTGGAATTTGCCCACGT
Band lengths:
352-793
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]