DreINT0096897 @ danRer10
Intron Retention
Gene
ENSDARG00000042816 | mmp9
Description
matrix metallopeptidase 9 [Source:ZFIN;Acc:ZDB-GENE-040426-2132]
Coordinates
chr8:24273764-24274708:+
Coord C1 exon
chr8:24273764-24273867
Coord A exon
chr8:24273868-24273949
Coord C2 exon
chr8:24273950-24274708
Length
82 bp
Sequences
Splice sites
5' ss Seq
AGGGTAAAT
5' ss Score
5.83
3' ss Seq
CTTCATTTCATGTTTTGCAGGAT
3' ss Score
9.24
Exon sequences
Seq C1 exon
ACTTGATGTAAAGGCTCAGCTGATTGACAGAGGATACCCTCGATTCACTGATGCAGCTTTCGGTGGAGTGCCCGTTGATTCACATGATGTATTCCTCTACAAGG
Seq A exon
GTAAATTAAATTACTTTTAGAATTAAAACTAATTCAATGAATGATCTCTTTTTTTATGACATCTTCATTTCATGTTTTGCAG
Seq C2 exon
GATTCTTCTACTTCTGCCGGGAGAGCTTCTACTGGAGAATGAATGCCAAACGGCAGGTTGACCGAGTCGGTTATGTGAAGTACGACCTCCTGAAATGCAGTGACATTCATTCTCTATAGACCTTCGACATCCTAATCTGATGACAGAGCCCTTTTTTAACAGGGAAACCGTTTCTCTTCAGTGTAAAATGTAGCGAGGAAGACACAGACAGAATGTATTAAATTTCAAGTGTCTGTTAAAGGGATTTTGACTTTAACTGTTATAGGAAAAGAACAGTTTTAACACTGAAATTATCATAGGCACATGAGACGGGATGTTAGGCATATTTGTCCGTCAGCTTTACCATGGTCTTATAATTTATTATTTCAGCTTCCCACATAACTGCTTTGGTCATGATGGGTTTCCTAATGGCACATTATTGTAGAAAACGAGGCAAAGCCCGTTTGACTTTAGGAATTAACTTTGTGCTTGTAAATGTGTGAGTGGAGTCTCCGCAGGAATGTTGTAGCCGATTTGTTGTGAACAAAGCACCCGTATTCTGCATTGACCCCATTCAGATGTTTTTGAATGCAAAGGTTTATTTTTAGCCTTAGAGCTAATGATGGGGATTGCAGATTTTGCCATATTGTGAAATCATTTGCCTGGTGTAAATGATATTATTAATATTATTAATTTAATGTTCAACCTTCCACTTATTTATATTTTTATGTTTGTTGCAGTGTTTGTTTACTTAATAAATTTGTAAACAAGATCCTTTAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000042816:ENSDART00000062845:12
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0004514=Hemopexin=PD(53.3=66.7),PF0004514=Hemopexin=PU(20.6=19.4)
A:
NA
C2:
PF0004514=Hemopexin=PD(76.5=65.0)
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:
CCCTCGATTCACTGATGCAGC
R:
TGCATTTCAGGAGGTCGTACT
Band lengths:
167-249
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]