HsaINT0126526 @ hg19
Intron Retention
Gene
ENSG00000104368 | PLAT
Description
plasminogen activator, tissue [Source:HGNC Symbol;Acc:9051]
Coordinates
chr8:42037760-42038203:-
Coord C1 exon
chr8:42038008-42038203
Coord A exon
chr8:42037897-42038007
Coord C2 exon
chr8:42037760-42037896
Length
111 bp
Sequences
Splice sites
5' ss Seq
GAGGTAGGG
5' ss Score
7.81
3' ss Seq
TAAGGCTGTTTCTCCACCAGGTT
3' ss Score
7.97
Exon sequences
Seq C1 exon
CCACCTGCGGCCTGAGACAGTACAGCCAGCCTCAGTTTCGCATCAAAGGAGGGCTCTTCGCCGACATCGCCTCCCACCCCTGGCAGGCTGCCATCTTTGCCAAGCACAGGAGGTCGCCCGGAGAGCGGTTCCTGTGCGGGGGCATACTCATCAGCTCCTGCTGGATTCTCTCTGCCGCCCACTGCTTCCAGGAGAG
Seq A exon
GTAGGGGCTCGGAAACCCAGTTGGTTTTTCCACCCTCTAACGCCTAGAAACCAAGCCCTTTAGGGGAAATCCCACAGCAAAAAAAGCATTCTAAGGCTGTTTCTCCACCAG
Seq C2 exon
GTTTCCGCCCCACCACCTGACGGTGATCTTGGGCAGAACATACCGGGTGGTCCCTGGCGAGGAGGAGCAGAAATTTGAAGTCGAAAAATACATTGTCCATAAGGAATTCGATGATGACACTTACGACAATGACATTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000104368-PLAT:NM_033011:9
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:
PF0008921=Trypsin=PU(20.7=77.3)
A:
NA
C2:
PF0008921=Trypsin=FE(18.7=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CCAGCCTCAGTTTCGCATCAA
R:
AAATTTCTGCTCCTCCTCGCC
Band lengths:
247-358
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)