HsaINT0090360 @ hg19
Intron Retention
Gene
ENSG00000130702 | LAMA5
Description
laminin, alpha 5 [Source:HGNC Symbol;Acc:6485]
Coordinates
chr20:60885234-60885628:-
Coord C1 exon
chr20:60885475-60885628
Coord A exon
chr20:60885368-60885474
Coord C2 exon
chr20:60885234-60885367
Length
107 bp
Sequences
Splice sites
5' ss Seq
TAGGTCTGT
5' ss Score
3.44
3' ss Seq
ATCACAACCCCTCCCCGCAGACC
3' ss Score
10.45
Exon sequences
Seq C1 exon
GTGACCGTCGGGTTCAGCGGCTGTGTGAAGAGACTGAGGCTGCACGGGAGGCCCCTGGGGGCCCCCACACGGATGGCAGGGGTCACACCCTGCATCTTGGGCCCCCTGGAGGCGGGCCTGTTCTTCCCAGGCAGCGGGGGAGTTATCACTTTAG
Seq A exon
GTCTGTGGGTGCTGGCATCCCAGGCCTCAGCAGGGCAGGGCAGGGGGCTCCAGGAGGTTCTGGGGAGGGGCCCCCCCTTTCTTCTCCATCACAACCCCTCCCCGCAG
Seq C2 exon
ACCTCCCAGGAGCTACACTGCCTGATGTGGGCCTGGAACTGGAGGTGCGGCCCCTGGCAGTCACCGGACTGATCTTCCACTTGGGCCAGGCCCGGACGCCCCCCTACTTGCAGTTGCAGGTGACCGAGAAGCAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000130702-LAMA5:NM_005560:76
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.038 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0221019=Laminin_G_2=PD(12.3=30.8)
A:
NA
C2:
PF0221019=Laminin_G_2=PU(23.2=64.4)
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:
AAGAGACTGAGGCTGCACGG
R:
CTTCTCGGTCACCTGCAACTG
Band lengths:
258-365
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)