HsaINT0103994 @ hg19
Intron Retention
Gene
ENSG00000087245 | MMP2
Description
matrix metallopeptidase 2 (gelatinase A, 72kDa gelatinase, 72kDa type IV collagenase) [Source:HGNC Symbol;Acc:7166]
Coordinates
chr16:55519211-55519689:+
Coord C1 exon
chr16:55519211-55519339
Coord A exon
chr16:55519340-55519515
Coord C2 exon
chr16:55519516-55519689
Length
176 bp
Sequences
Splice sites
5' ss Seq
AAGGTGAGA
5' ss Score
8.68
3' ss Seq
CCTTCCATGTCACTCTTTAGTGG
3' ss Score
6.06
Exon sequences
Seq C1 exon
AGCATGGCGATGGATACCCCTTTGACGGTAAGGACGGACTCCTGGCTCATGCCTTCGCCCCAGGCACTGGTGTTGGGGGAGACTCCCATTTTGATGACGATGAGCTATGGACCTTGGGAGAAGGCCAAG
Seq A exon
GTGAGAAAGGGGCCCTCTGCATGCCCCAGACCTTCTCTCCTGTCCTCTCTCCACTCCATTTGCTTGGACCAGAGAGGTGGGAGGGGAGGAAAGTCACACATCTGGGTGAGTCAGAATCTTGGTCTCCAAAGAAGGCCTGGAGAAGTCCAACCTCCCCCTTCCATGTCACTCTTTAG
Seq C2 exon
TGGTCCGTGTGAAGTATGGGAACGCCGATGGGGAGTACTGCAAGTTCCCCTTCTTGTTCAATGGCAAGGAGTACAACAGCTGCACTGATACCGGCCGCAGCGATGGCTTCCTCTGGTGCTCCACCACCTACAACTTTGAGAAGGATGGCAAGTACGGCTTCTGTCCCCATGAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000087245-MMP2:NM_001127891:4
Average complexity
IR-S
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:
PF0041319=Peptidase_M10=PD(22.1=89.5)
A:
NA
C2:
PF0041319=Peptidase_M10=PD(31.3=81.0),PF0004014=fn2=WD(100=72.4)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CCTTTGACGGTAAGGACGGAC
R:
AAGTTGTAGGTGGTGGAGCAC
Band lengths:
247-423
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Autistic and control brains
- Pre-implantation embryo development
Other AS DBs:
FasterDB (Includes CLIP-seq data)
AS-ALPS (AS-induced ALteration of Protein Structure, links to PINs)
APPRIS (Selection of principal isoform)
DEU primates (Only for human)