HsaINT0090288 @ hg19
Intron Retention
Gene
ENSG00000130702 | LAMA5
Description
laminin, alpha 5 [Source:HGNC Symbol;Acc:6485]
Coordinates
chr20:60920874-60921271:-
Coord C1 exon
chr20:60921137-60921271
Coord A exon
chr20:60920934-60921136
Coord C2 exon
chr20:60920874-60920933
Length
203 bp
Sequences
Splice sites
5' ss Seq
ACCGTGAGC
5' ss Score
4.78
3' ss Seq
TGCGTGTCTCTTCCCCTCAGCGA
3' ss Score
10.19
Exon sequences
Seq C1 exon
GCTGCAACTGCGAGTCCGACTTCACGGATGGCACCTGCGAGGACCTGACGGGTCGATGCTACTGCCGGCCCAACTTCTCTGGGGAGCGGTGTGACGTGTGTGCCGAGGGCTTCACGGGCTTCCCAAGCTGCTACC
Seq A exon
GTGAGCACCTGCCAGGGGCATCCAAACAGACACCACTGCCTGCTGGACTCCGGGAGCCCTGCAGGGGGTGGAGGGGTTCCCCGGGATGGACCATGTTATCCTGCCTGCATCTCCGATTGTGCTGAGAGACCAAGGGTGGCAGGGGGTGTAGGGTGCTAGGGTTCTGAGCAGACCTGGCCAACATGCGTGTCTCTTCCCCTCAG
Seq C2 exon
CGACGCCCTCGTCCTCCAATGACACCAGGGAGCAGGTGCTGCCAGCCGGCCAGATTGTGA
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000130702-LAMA5:NM_005560:10
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=0.196
Domain overlap (PFAM):
C1:
PF0005319=Laminin_EGF=PU(88.0=95.7)
A:
NA
C2:
PF0005319=Laminin_EGF=PD(10.0=23.8)
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:
CAACTGCGAGTCCGACTTCAC
R:
CACAATCTGGCCGGCTGG
Band lengths:
190-393
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
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)