HsaINT0104092 @ hg19
Intron Retention
Gene
ENSG00000100985 | MMP9
Description
matrix metallopeptidase 9 (gelatinase B, 92kDa gelatinase, 92kDa type IV collagenase) [Source:HGNC Symbol;Acc:7176]
Coordinates
chr20:44639782-44640386:+
Coord C1 exon
chr20:44639782-44639955
Coord A exon
chr20:44639956-44640212
Coord C2 exon
chr20:44640213-44640386
Length
257 bp
Sequences
Splice sites
5' ss Seq
AGAGTGAGT
5' ss Score
7.36
3' ss Seq
CCACATCCTCCTCGCCCCAGGAC
3' ss Score
8.04
Exon sequences
Seq C1 exon
TGGTTCCAACTCGGTTTGGAAACGCAGATGGCGCGGCCTGCCACTTCCCCTTCATCTTCGAGGGCCGCTCCTACTCTGCCTGCACCACCGACGGTCGCTCCGACGGCTTGCCCTGGTGCAGTACCACGGCCAACTACGACACCGACGACCGGTTTGGCTTCTGCCCCAGCGAGA
Seq A exon
GTGAGTGAGGGGGCTCGCCGAGGGCTGGGGGCGCCCACCACCCTTGATGGTCCTGGGTTCTAATTCCAGCTCTGCCACTAGTGCTGTGTGGCCTGCAATTCACCCTCCCGCACTCTGGGCCCAATTTTCTCATCTGAGAAATGATGAGAGATGGGATGAACTGCAGACCATCCATGGGTCAAAGAACAGGACACACTTGGGGGTTATAATGTGCTGTCTCCGCCTTCTCCCCCTTTCCCACATCCTCCTCGCCCCAG
Seq C2 exon
GACTCTACACCCAGGACGGCAATGCTGATGGGAAACCCTGCCAGTTTCCATTCATCTTCCAAGGCCAATCCTACTCCGCCTGCACCACGGACGGTCGCTCCGACGGCTACCGCTGGTGCGCCACCACCGCCAACTACGACCGGGACAAGCTCTTCGGCTTCTGCCCGACCCGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000100985-MMP9:NM_004994:5
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=FE(17.6=100),PF0004014=fn2=WD(100=71.2)
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
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GCCACTTCCCCTTCATCTTCG
R:
CAGAAGCCGAAGAGCTTGTCC
Band lengths:
298-555
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Genotype-Tissue Expression Project (GTEx)
- 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)