DreINT0096895 @ danRer10
Intron Retention
Gene
ENSDARG00000042816 | mmp9
Description
matrix metallopeptidase 9 [Source:ZFIN;Acc:ZDB-GENE-040426-2132]
Coordinates
chr8:24272185-24273158:+
Coord C1 exon
chr8:24272185-24272318
Coord A exon
chr8:24272319-24273007
Coord C2 exon
chr8:24273008-24273158
Length
689 bp
Sequences
Splice sites
5' ss Seq
CAGGTTATT
5' ss Score
3.49
3' ss Seq
TCCGTATTTAATCCACACAGAGA
3' ss Score
5.19
Exon sequences
Seq C1 exon
GCGCTACTGGAAGATCTCAGGCAATGGTGAACGCAAAGGTCCTTTCATGATCTCTGCGAAGTGGCCTGCTCTCCCAGCTGTCATCAACTCTGCCTTTGAGGACCACCTCACCAAAAAGATCTACTTCTTCTCAG
Seq A exon
GTTATTATTTACTTGGTTGAGATATTTTGCCATTTGCAGTAATATTGTAATCAAAATTTTAACTGCAAGCTGACTTTACTGAAGGTATTTTTTTCCCCCAATTTCTGTTTTACGAAGAGAAGATTTTATCATCACATTTCTAAACATGATAGTTTTAATAACTCATTTCTAACAACTGATTTATTTCATCTTTGCCATGATGACAGTAAATAATATTTTACCATCGAAATACAGCTTAAAGGGGCTAATAATATTGACCTTAAAATGTTTTTTTTTTTTTTACATAAAAAACTGCTTTTATTCTACCCAAAATAAAACAAATAAAACTTCAATCAGTTATAAAAGTTTTTGTTTTCTAAATAATTGGTATCACACTAGCAAGATTGCGACGGTTCCAAACAAAGCTTCAGCAGAACTTTTTTTTTTGCATCTCAGAGCAACACTACATTGATTAATCCTTAAATGATTCATTGATTCAGTCAGTCACAAAAGCAGTCGTTTGTCACAATTTCTACATCAATTAGTTGCTTTGAACAAATCATTTAATGGACGATTATCAACTCTTTATACCTGGAAATCTATCAAAAGCACACTCAGTATAATATTGTTTTGTTATTTTGGTCAATATTAAAATATATTGCACACCCCTAGTTCAGAAATATAATATCATCCGTATTTAATCCACACAG
Seq C2 exon
AGAGACAGTTCTGGGTTTACAGTGGAAATGATGTGCTTGGACCACGTAAAATCGAGAAGCTCGGCCTACCAAGCGACTTGGACAAAGTGGAAGGATCTATGCAGAGAGGAAAAGGCAAGGTGCTCCTGTTTAATGGAGAAAACTTCTGGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000042816:ENSDART00000062845:10
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0004514=Hemopexin=PD(60.5=56.5),PF0004514=Hemopexin=PU(40.5=37.0)
A:
NA
C2:
PF0004514=Hemopexin=PD(57.1=47.1),PF0004514=Hemopexin=PU(44.4=39.2)
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:
GCGCTACTGGAAGATCTCAGG
R:
AGTTTTCTCCATTAAACAGGAGCAC
Band lengths:
278-967
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]