RnoINT0093254 @ rn6
Intron Retention
Gene
ENSRNOG00000017539 | Mmp9
Description
matrix metallopeptidase 9 [Source:RGD Symbol;Acc:621320]
Coordinates
chr3:161417778-161418318:+
Coord C1 exon
chr3:161417778-161417917
Coord A exon
chr3:161417918-161418167
Coord C2 exon
chr3:161418168-161418318
Length
250 bp
Sequences
Splice sites
5' ss Seq
CTGGTTAGT
5' ss Score
6.32
3' ss Seq
ATGACCCTTCTCTTTCGTAGGGC
3' ss Score
9.67
Exon sequences
Seq C1 exon
TCGGTATTGGAAGTTCTCGAATCACGGAGGAAGCCAATTGCAGGGCCCCTTTCTTATTGCCCGCACGTGGCCAGCTTTGCCTGCAAAGTTGAACTCAGCCTTTGAGGATCCGCAGTCCAAGAAGATTTTCTTCTTCTCTG
Seq A exon
GTTAGTGCGAGCGTTTCTAGCTCATCTATTTCTCCGAACTCATCAGCTTAGGACAGAGACCTAGTTTAACTGCGACTGCAAAAGTGCGCCCCCGCCTGGCTGATGCGATTTGACATCGGGGGAGGGGGTTGAATTTCAGTGCCCTTGAGTAGCTCTGATACTTGGTCTCTGGCTTATCCCTCCTAACTCTCAAAGAGACTGTGCCCCCACCTTTGTGTCCACTGACCAATATGACCCTTCTCTTTCGTAG
Seq C2 exon
GGCGCAAAATGTGGGTGTACACAGGCCAGTCGGTGCTGGGCCCCAGGAGTCTGGATAAGTTGGGTCTAGGCTCAGAGGTAACCCTGGTCACCGGACTTCTCCCGCGTCGTGGAGGGAAGGCTCTGCTGATCAGCCGGGAACGTATCTGGAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000017539:ENSRNOT00000023965:10
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.021 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0004514=Hemopexin=PD(62.2=58.3),PF0004514=Hemopexin=PU(40.5=35.4)
A:
NA
C2:
PF0004514=Hemopexin=PD(57.1=47.1)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TGGAAGTTCTCGAATCACGGA
R:
TTCCAGATACGTTCCCGGCT
Band lengths:
284-534
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]