HsaINT0104092 @ hg38
Intron Retention
Gene
ENSG00000100985 | MMP9
Description
matrix metallopeptidase 9 [Source:HGNC Symbol;Acc:HGNC:7176]
Coordinates
chr20:46011143-46011747:+
Coord C1 exon
chr20:46011143-46011316
Coord A exon
chr20:46011317-46011573
Coord C2 exon
chr20:46011574-46011747
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:ENST00000372330:5
Average complexity
IR
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