HsaINT0104096 @ hg19
Intron Retention
Gene
ENSG00000100985 | MMP9
Description
matrix metallopeptidase 9 (gelatinase B, 92kDa gelatinase, 92kDa type IV collagenase) [Source:HGNC Symbol;Acc:7176]
Coordinates
chr20:44641894-44642435:+
Coord C1 exon
chr20:44641894-44642173
Coord A exon
chr20:44642174-44642295
Coord C2 exon
chr20:44642296-44642435
Length
122 bp
Sequences
Splice sites
5' ss Seq
TGGGTGAGG
5' ss Score
6.74
3' ss Seq
TTCCCTCCTCGCTTTCTCAGGAA
3' ss Score
11.22
Exon sequences
Seq C1 exon
GTCCTCGCCCTGAACCTGAGCCACGGCCTCCAACCACCACCACACCGCAGCCCACGGCTCCCCCGACGGTCTGCCCCACCGGACCCCCCACTGTCCACCCCTCAGAGCGCCCCACAGCTGGCCCCACAGGTCCCCCCTCAGCTGGCCCCACAGGTCCCCCCACTGCTGGCCCTTCTACGGCCACTACTGTGCCTTTGAGTCCGGTGGACGATGCCTGCAACGTGAACATCTTCGACGCCATCGCGGAGATTGGGAACCAGCTGTATTTGTTCAAGGATGG
Seq A exon
GTGAGGAGGCGGGGTTGTGTGGATGCGGGAGGGGGCTTTGCGGAGGGGCTGCCCGTCCCTTCCCGCCCACTGGCCCTGTGTCCAAGGCTTAGAGCCCGTCCTTTCCCTCCTCGCTTTCTCAG
Seq C2 exon
GAAGTACTGGCGATTCTCTGAGGGCAGGGGGAGCCGGCCGCAGGGCCCCTTCCTTATCGCCGACAAGTGGCCCGCGCTGCCCCGCAAGCTGGACTCGGTCTTTGAGGAGCGGCTCTCCAAGAAGCTTTTCTTCTTCTCTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000100985-MMP9:NM_004994:9
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.713 A=NA C2=0.042
Domain overlap (PFAM):
C1:
PF0041319=Peptidase_M10=PD(0.1=0.0),PF048867=PT=WD(100=38.3),PF0004514=Hemopexin=PU(35.6=17.0)
A:
NA
C2:
PF0004514=Hemopexin=PD(62.2=58.3),PF0004514=Hemopexin=PU(40.5=35.4)
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:
CCCTTCTACGGCCACTACTGT
R:
AGAAAAGCTTCTTGGAGAGCCG
Band lengths:
242-364
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)