HsaINT0104088 @ hg19
Intron Retention
Gene
ENSG00000100985 | MMP9
Description
matrix metallopeptidase 9 (gelatinase B, 92kDa gelatinase, 92kDa type IV collagenase) [Source:HGNC Symbol;Acc:7176]
Coordinates
chr20:44643010-44645200:+
Coord C1 exon
chr20:44643010-44643113
Coord A exon
chr20:44643114-44644888
Coord C2 exon
chr20:44644889-44645200
Length
1775 bp
Sequences
Splice sites
5' ss Seq
GAGGTGAGG
5' ss Score
8.41
3' ss Seq
TGCCTGCCTGTCTCCTGCAGAGA
3' ss Score
11.05
Exon sequences
Seq C1 exon
GTTCGACGTGAAGGCGCAGATGGTGGATCCCCGGAGCGCCAGCGAGGTGGACCGGATGTTCCCCGGGGTGCCTTTGGACACGCACGACGTCTTCCAGTACCGAG
Seq A exon
GTGAGGGCTGAGGAGGATCCCTTCGTGAGACACCACACTAAGCTCCTCTTAGTGAGTGGTCAAATTCTGAGCGAGGAAGAAAAAGCCCTTGGAAATGGAAACAAATGCCCCAGCACAGACAAGATCCCAGCAGAGGCAGAGGCCTTCTCCAGGTCATTTAGGAAGTCAGGGATGCAACCAAGACCAGGACCCAGATTTCCTGCCTCCCCGGCTGGAAGCTCTTTCTCCTTCAGTACAGGACGGCAGGTGGTTTGTATGGAAGCTCAGTTATTAGACAACAGTCATCAAGTGCCGATAATGTGCCAGGCACTGTGCTACAGGGAGAGATAAGACAATTCACAGCTCTGTGACTTTGGGCAAGTCACTGCTTCTCTACTCTTCGAGCCTCAGTTTCCCCATCTGTAATATGGGGACTATAGCTGGAATTACACTTGACTTCCCTTTCTTACCAGTCACATCCAAACAGTTGACAAGGTGAACAAGATTTCCTGCCACCAAAATCTTTTTCGAGTCTGTCATTTTTTTTGCCATCTTCTTTATAAACACCCCAGCCCAAACCATACTGGCTGTCCAGGACCTTTAACAAATTCCATGAGATTAGAGAGGGGGTAGGAGTGAAGGGCAATGGTCTTGGGAGTGACCCCAGATGAATTCCAAGGTCAAAGAAATTAAGAGGATCTGACACTCCACCCCCGTGTTCTCATCTCTTCCCACTCCTCCTGTTATTTACTCTGCTCCACCCACACTGGCTGCTCTTTGAACAGATCAAGGTCATTCCTAGCTTACAGCCTTTGTGCCAGTTGTTCCCTCTGTCTGGAAAGCTTCCCCTCCAGATTGTCACTGGGCCATCCCACTGTCTTCCTTCAGGTTTCAGTGCTAAGGCCATTGCTTCAATGAGGCCTTCTTTGATGCTTATTATCTATTTACTTGTTTTTATTTTCTCCATAGCTTTCTATATTTTCTTTTTTTTTCTTTTTTCTTTTTTTTTTTTTTTGAGATGGAGTCTTGCTCTGTCGCCCAGGCTGGAGTGCAGTGGCACGATCTCAGCTCACTGCAACCTCCGCCTCCCGGGTTCAAGCGATTCTCCTGCCTCAGCCTCCCAAGTAGCTGGGATTACAGGTGCCTGCCACCACGCTTGGCTAATTTTTTGTATTTTTTAGTAGAGACGGGGTTTCACCATCTTGGCCAGGCTGGTCTTGAACTCCTGACCTCGTGATCCACCCGCCTCAGCCTCCCAAAGTGCTGGGATTACAGGCATGAGCCACCGCACCCAGCCGCTTTCTATATTTTCAAAACCAATCTCATTTATTTATGTGTTTGCTTAATTGTCTCTTGCCTCACTAGAGTGTAAGCACCAAGATAATTGAGATCATGCCTGCATTTTTTCTGCTTATCCCCAGTATCTTGAACAAAGCACATAGTAGATGCTCAGTAAATGATGAATGAACAGATTTGTTCAATGAATGAGCGTTGAATGAATTGTTCTGAGCATTAAGATAGTTGGTCTATTCATTTGTTAATTCATTCACAAAATGTGTATGGTGTACCTACTGTGTGCTAGGCTCTGTGGCAGTGCTTTGGGCACTGAGGTCTGTGCCCTCCAGCATCTCACAGAACCTCACAGCATCTCACAGGTTGGGGGGATGGAGGTGATATGTGAAAACCTTAGAAAGTTCTAGAAATGGCAGAAGAGATGGTTGTCAAGATCTTGTTCCTATTTCTGTATATGTGGGAGAATTAGAATCACTCCTCTTATGCCTGCCTGTCTCCTGCAG
Seq C2 exon
AGAAAGCCTATTTCTGCCAGGACCGCTTCTACTGGCGCGTGAGTTCCCGGAGTGAGTTGAACCAGGTGGACCAAGTGGGCTACGTGACCTATGACATCCTGCAGTGCCCTGAGGACTAGGGCTCCCGTCCTGCTTTGGCAGTGCCATGTAAATCCCCACTGGGACCAACCCTGGGGAAGGAGCCAGTTTGCCGGATACAAACTGGTATTCTGTTCTGGAGGAAAGGGAGGAGTGGAGGTGGGCTGGGCCCTCTCTTCTCACCTTTGTTTTTTGTTGGAGTGTTTCTAATAAACTTGGATTCTCTAACCTTTA
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000100985-MMP9:NM_004994:12
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0004514=Hemopexin=PD(50.0=61.1),PF0004514=Hemopexin=PU(18.2=22.2)
A:
NA
C2:
PF0004514=Hemopexin=PD(79.5=87.5)
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:
CAGATGGTGGATCCCCGGAG
R:
AAAGGTGAGAAGAGAGGGCCC
Band lengths:
353-2128
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)