HsaINT0103989 @ hg19
Intron Retention
Gene
ENSG00000087245 | MMP2
Description
matrix metallopeptidase 2 (gelatinase A, 72kDa gelatinase, 72kDa type IV collagenase) [Source:HGNC Symbol;Acc:7166]
Coordinates
chr16:55530838-55532360:+
Coord C1 exon
chr16:55530838-55530974
Coord A exon
chr16:55530975-55532200
Coord C2 exon
chr16:55532201-55532360
Length
1226 bp
Sequences
Splice sites
5' ss Seq
CAGGTGTGT
5' ss Score
6.99
3' ss Seq
ACCCTTTGCTTCCACCCCAGGGA
3' ss Score
8.51
Exon sequences
Seq C1 exon
GTTCATTTGGCGGACTGTGACGCCACGTGACAAGCCCATGGGGCCCCTGCTGGTGGCCACATTCTGGCCTGAGCTCCCGGAAAAGATTGATGCGGTATACGAGGCCCCACAGGAGGAGAAGGCTGTGTTCTTTGCAG
Seq A exon
GTGTGTGGGAAGCACCCTTCCTTGGCCCTCAGCTCCACAGGGCTCTGCACCAGGGCTCCTGGGTGTCCCAGGCTCACTCCCCCTCTCAAACCACAGTTCCTATGCACCCGTGGGTGCTCCCTTTCCTTTATGGATTCATTCTTTCAACATTATTTCCTGAAGTGCGCAGCTCCTCTGGGAGATTGGTTCCGACACCCAACATCAGATAGCATTAACCCTCAGTGTACACATTTCATTTTCTTAATTCTTTTCAATCCGTCTCATTTCTTTTCTAGAAGAAAAAAAGTCTCAGTTTAGTGCTGGTGTGTCCCTAACGCCTTTGTAGTGATACAGTCTTTGGCAGGTAACAGTTTTAGTTCGAATGTTTTAAAGAATATTTGTTTTCATTTTTACTTTTAGACATAAATTGGTTTTAACAGAGGCAGTTAGTTATAATAGTGTGGAGTTTCAAATCAGGACAGAAACGGATTATTCAGTAACTGATATTTTGACAGTCAAAAAACATTTTTTAATAAATTTATTTTTAAAGATTTCAAAATGAATTCACTGAAAGCAGAATGTTAAGTAAATAATAGTACAGGGAGCCCCTAGAAGTGGTAGAAATCATCAAGGTGAGGTCTGTATGGCTAAGGTTTACTCATTTAACATTTATTGGAGCATTTCCATGCGCTGGGCTTTGCCATACCCTGGGGATACAAGCTCTGCCTTCGCGATGCTCACAAACCACTCAGGGAGACAGACAGCTGGGCTCTTATGAGGGGTAAAGAAGGATTTAGGAGGTCCCTGTCCTGGTCTGAGGTGGGATCCTAGAGAAGATAAAGGCTCAGCCAAGACTATTGTCTCCACCACCTGGCTCCCACCTCCCCCAATCCACCGTAATCATGGGTCCCGGAGAGGACAACTGCTGGCTCCTAGGGCACCTTTTTGCAAATTAGCAAAAGGTGCCTCTTTATGACAGCAAGGCCCTTAGAGTGCACGACTTGGTGAGCAGAGTGTGAGCTGGATTTATCCCCCAACTCATGTCCTTGACCAGGCACCTTCTGTAATTGACTTCTAAAGCCCTCTGTGTGAGCCCTGATTCTGGGCACTGCAACCAGGAGTGAGCAGGAAGTTGCACTCTGTTGGGAATGGCTGCAGTGGGGCCCGTGGACAGACAGATGATGGGAGGAACAGGCTGGCCTAGGGCATGTCAGCACCAGCCAACACACCCTTTGCTTCCACCCCAG
Seq C2 exon
GGAATGAATACTGGATCTACTCAGCCAGCACCCTGGAGCGAGGGTACCCCAAGCCACTGACCAGCCTGGGACTGCCCCCTGATGTCCAGCGAGTGGATGCCGCCTTTAACTGGAGCAAAAACAAGAAGACATACATCTTTGCTGGAGACAAATTCTGGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000087245-MMP2:NM_001127891:10
Average complexity
IR-S
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(61.4=57.4),PF0004514=Hemopexin=PU(38.6=36.2)
A:
NA
C2:
PF0004514=Hemopexin=PD(59.1=48.1),PF0004514=Hemopexin=PU(45.8=40.7)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TTCATTTGGCGGACTGTGACG
R:
CTCCAGAATTTGTCTCCAGCA
Band lengths:
296-1522
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)