DreINT0096832 @ danRer10
Intron Retention
Gene
ENSDARG00000017676 | mmp2
Description
matrix metallopeptidase 2 [Source:ZFIN;Acc:ZDB-GENE-030131-9123]
Coordinates
chr7:35156472-35156893:-
Coord C1 exon
chr7:35156765-35156893
Coord A exon
chr7:35156646-35156764
Coord C2 exon
chr7:35156472-35156645
Length
119 bp
Sequences
Splice sites
5' ss Seq
AAGGTATCT
5' ss Score
7.56
3' ss Seq
TTCTCTCTCTTCTGACGTAGTGG
3' ss Score
6.99
Exon sequences
Seq C1 exon
AACATGGTGATGGTTATCCATTTGATGGCAAGGATGGTCTGCTGGCTCATGCATTTGCCCCTGGACCTGGTATTGGAGGAGACTCTCACTTTGATGATGATGAGCAGTGGACTTTAGGAGAAGGACAAG
Seq A exon
GTATCTGCAAATGTCTTGATTCTAGTCACTTGTAGTCTGTAGTATATTAAAGTAATTGTTTTTGATTGTTTGTTTAATGTCTTACAATGGTCTCTCTCCTTCTCTCTCTTCTGACGTAG
Seq C2 exon
TGGTAAAGGTGAAGTACGGTAATGCTGAGGGCGAGTTCTGTAAGTTTCCATTTTTGTTCATGGGTAAAGAGTACAACAGCTGCACCTCTCAGGGTCGAGATGATGGGTTCCTTTGGTGCTCCACCACATACAACTTTGATGATGATGGAAAGTACGGCTTCTGTCCCCATGAGC
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000017676:ENSDART00000026712:4
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.068 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0041319=Peptidase_M10=FE(13.1=100)
A:
NA
C2:
PF0041319=Peptidase_M10=FE(17.6=100),PF0004014=fn2=WD(100=71.2)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
ATTTGCCCCTGGACCTGGTAT
R:
GGGACAGAAGCCGTACTTTCC
Band lengths:
244-363
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]