HsaINT0104087 @ hg38
Intron Retention
Gene
ENSG00000100985 | MMP9
Description
matrix metallopeptidase 9 [Source:HGNC Symbol;Acc:HGNC:7176]
Coordinates
chr20:46014124-46014474:+
Coord C1 exon
chr20:46014124-46014274
Coord A exon
chr20:46014275-46014370
Coord C2 exon
chr20:46014371-46014474
Length
96 bp
Sequences
Splice sites
5' ss Seq
GAGGTGAGC
5' ss Score
8.7
3' ss Seq
TCCTCCGCGCCTGCCCGCAGGTT
3' ss Score
10.79
Exon sequences
Seq C1 exon
GGCGCCAGGTGTGGGTGTACACAGGCGCGTCGGTGCTGGGCCCGAGGCGTCTGGACAAGCTGGGCCTGGGAGCCGACGTGGCCCAGGTGACCGGGGCCCTCCGGAGTGGCAGGGGGAAGATGCTGCTGTTCAGCGGGCGGCGCCTCTGGAG
Seq A exon
GTGAGCGCCGCCGCGGCCGCCGGCAGGGGGAGCCCGGGCGCCGTCGGTCCGTCCGCTAGCCGGCTCAGCACCTGTCTCCTCCGCGCCTGCCCGCAG
Seq C2 exon
GTTCGACGTGAAGGCGCAGATGGTGGATCCCCGGAGCGCCAGCGAGGTGGACCGGATGTTCCCCGGGGTGCCTTTGGACACGCACGACGTCTTCCAGTACCGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000100985:ENST00000372330:11
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:
PF0004514=Hemopexin=PD(57.1=47.1),PF0004514=Hemopexin=PU(47.7=41.2)
A:
NA
C2:
PF0004514=Hemopexin=PD(50.0=61.1),PF0004514=Hemopexin=PU(18.2=22.2)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GTGGGTGTACACAGGCGC
R:
GATCCACCATCTGCGCCTTC
Band lengths:
170-266
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