RnoINT0093189 @ rn6
Intron Retention
Gene
ENSRNOG00000016695 | Mmp2
Description
matrix metallopeptidase 2 [Source:RGD Symbol;Acc:621316]
Coordinates
chr19:15556362-15557644:-
Coord C1 exon
chr19:15557489-15557644
Coord A exon
chr19:15556504-15557488
Coord C2 exon
chr19:15556362-15556503
Length
985 bp
Sequences
Splice sites
5' ss Seq
ATGGTAAGC
5' ss Score
9.26
3' ss Seq
GTTGTCTCCCCATTCCTTAGGGC
3' ss Score
9.31
Exon sequences
Seq C1 exon
GATATAGCCTATTCCTTGTGGCAGCCCATGAGTTCGGCCATGCCATGGGGCTGGAACACTCACAGGACCCTGGAGCTTTGATGGCCCCTATCTACACCTACACCAAGAACTTCCGACTATCCAATGATGACATCAAGGGGATCCAGGAGCTCTATG
Seq A exon
GTAAGCCATAGCTTGATGGCCTCTGAGGGGAGAGGTGTCTGCAAGTATCCCACAGCCTAGGTGAGAGGACACAGAAGTGGAAAATGCCAGACCTCATCTAGTCAGAATGGCCGGAGACATCATCAGGGGACATGGCTTGTCCCTGGTCCTCAGGCTCCAGAGTAATGTTCCGAAGGGCTGCTCAGACAGCCCTGTCCTTTCTAAACACTAGTTGTCCATGGCCCTCTTGGTTCCCCATTTCCAGGGCTTTCCATGTGCTAGGTATATGAGCTGAGACTGGAGAAAGGAAGTCGGTCTGGCCCAAGGTCAACTACATTTCAGCAGCCAGGTAGGGTTTAGGATCCCGAAGAGTGAGCGGCCTATAGGGCAGGATTTTCTCTGGCACGGAAAGGGTGCTGCTAGTTCTCCTAAGATGCTGTTGTTTCATTTTGCCATAGAAACATAATAACTGCTTCCTGCCACCAATGATGCTTTTTTGTCTGTGCTTTCAGTGAGGTTAGAGGCTTAAAAATCAGTCAATTTCTTTAAAAAGAAATCAATTATAGAATAGTCCTAGTGGTTCCTGGCCCAGGCCAAGCAGTAAAAATAGGGAAATCCATGGACTCTGAACTCAGGAAAGAATCAGAGATATAGACAGTGATGTGTGACATTGAAGTCCTACTAAGGACACATGCTGGTCGAAATGCTGCAACAGTTCACCTCCCTAGACTCCACTGTTGCTCATCCTTAGGAATACAAAAGCAAATCCTTAAGAAAGTGCCACACCTCTACTGACACCAGCCAGCCTTCTCTGTTCTTAAAGGGAGAGCCCACAAAAGATTCAAGTGTCTGTTCCCCTCCCTAAGCTCAGGCTGCCCCAAGGTAGACTTTCTTCTCTTTTTTGTAGCCTTAGCAGATTAAGTGAGCAGTATTGGGGTTCCAGCCTAGTGATGAGAAGCCTTGTTGCTGGGGAGAGTCTAGGGACAGTTGTCTCCCCATTCCTTAG
Seq C2 exon
GGCCCTCCCCTGATGCTGATACTGACACTGGTACTGGACCCACGCCTACACTGGGACCTGTCACTCCCGAGATCTGCAAGCAAGACATTGTCTTTGATGGCATTGCTCAGATCCGTGGTGAGATCTTCTTCTTCAAGGATCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000016695:ENSRNOT00000022679:8
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.057 A=NA C2=0.417
Domain overlap (PFAM):
C1:
PF0041319=Peptidase_M10=FE(15.8=100)
A:
NA
C2:
PF0041319=Peptidase_M10=PD(0.1=0.0),PF0004514=Hemopexin=PU(35.6=33.3)
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:
TAGCCTATTCCTTGTGGCAGC
R:
CGATCCTTGAAGAAGAAGATCTCACC
Band lengths:
294-1279
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]