HsaINT0104085 @ hg19
Intron Retention
Gene
ENSG00000100985 | MMP9
Description
matrix metallopeptidase 9 (gelatinase B, 92kDa gelatinase, 92kDa type IV collagenase) [Source:HGNC Symbol;Acc:7176]
Coordinates
chr20:44637547-44638737:+
Coord C1 exon
chr20:44637547-44637703
Coord A exon
chr20:44637704-44638504
Coord C2 exon
chr20:44638505-44638737
Length
801 bp
Sequences
Splice sites
5' ss Seq
GAGGTGGGC
5' ss Score
6.32
3' ss Seq
GTGTGTCCCTTCATCCACAGGAA
3' ss Score
11.65
Exon sequences
Seq C1 exon
AGACACCTCTGCCCTCACCATGAGCCTCTGGCAGCCCCTGGTCCTGGTGCTCCTGGTGCTGGGCTGCTGCTTTGCTGCCCCCAGACAGCGCCAGTCCACCCTTGTGCTCTTCCCTGGAGACCTGAGAACCAATCTCACCGACAGGCAGCTGGCAGAG
Seq A exon
GTGGGCAAACACCTAGTCTAGAGTTGGGGAGGGCTGTCCGTGAGGGTGTTGAGTGTCCCAGAGAGGATGCAGGGCCTCAGAGGAGATGCTTTAGGGGTGTGTTGGTGGTGATGGGCGTATCTGAAGAACAGAGGTGTCCAGGGTTAGGCAGTGGGGGGTCTTGTGGAGGCTTTGAGCAGTGATGGCCAGAAATGGGCAATGGGGCTTTCCTAGGTGGGAAATGGGAAATGGTTTGGGGTGGGGGAGGCATTGGAGGGTTCTGGGGTAAGCATAGGCTGGGAGTGAACAGGGGCAAACCTTATGCAGCTGTGGGGTAGAAATGGGCTAGAGGCATCCAGGGGTGAGAAGGAGCTGAGGATGTCTAAGGAGGGGAGATCCCTGGGTGGTCAGAAAGCACTGGTGTCTGGAAAGCATTTAATGCTTTATTAAATGTTAGTCCCTGCTGGGCATGACGGCTCACACTTGTAATCCCAGCACTTTGGGAGGCTGAGGTGGTAGGATCGCTGAAGCTCAGGAGTTTGAGCCCAGCCTAGGCAACATAGTAAGATCCTGTCTCTACAAAAAAATTAAAGAAATAGCCAGGCACAGTGATGTGCACCTGTAGTTCCAGCTATGCAGAAGGCTGAGATGGGAGGATCGCTTGAGTCCAGGAGGTCCAGGCTGCAGTGGGCTGATACCGTCTCTCCGAAAAAGAAAAAGAAAAAAGACTCCCTCCATGAGTGTCTGGAGGGAGTCCTTTGGCCCCAGCTGGGCAGAGAAAGGGGTCAGAGATCTGGCATGTGTGTGTCCCTTCATCCACAG
Seq C2 exon
GAATACCTGTACCGCTATGGTTACACTCGGGTGGCAGAGATGCGTGGAGAGTCGAAATCTCTGGGGCCTGCGCTGCTGCTTCTCCAGAAGCAACTGTCCCTGCCCGAGACCGGTGAGCTGGATAGCGCCACGCTGAAGGCCATGCGAACCCCACGGTGCGGGGTCCCAGACCTGGGCAGATTCCAAACCTTTGAGGGCGACCTCAAGTGGCACCACCACAACATCACCTATTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000100985-MMP9:NM_004994:1
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0147113=PG_binding_1=PU(14.0=17.4)
A:
NA
C2:
PF0147113=PG_binding_1=PD(82.5=60.3),PF0041319=Peptidase_M10=PU(2.7=11.5)
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:
ACCTCTGCCCTCACCATGAG
R:
GTCGCCCTCAAAGGTTTGGAA
Band lengths:
354-1155
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)