HsaINT0090316 @ hg19
Intron Retention
Gene
ENSG00000130702 | LAMA5
Description
laminin, alpha 5 [Source:HGNC Symbol;Acc:6485]
Coordinates
chr20:60902585-60903066:-
Coord C1 exon
chr20:60902922-60903066
Coord A exon
chr20:60902726-60902921
Coord C2 exon
chr20:60902585-60902725
Length
196 bp
Sequences
Splice sites
5' ss Seq
AAGGTGAGT
5' ss Score
10.47
3' ss Seq
CACTGTCCTCTCATCCCTAGGAG
3' ss Score
10.88
Exon sequences
Seq C1 exon
GTGCAGACCCAACGTGACTGGGCGCCGCTGTGATACCTGCTCTCCGGGCTTCCATGGCTACCCCCGCTGCCGCCCCTGTGACTGTCACGAGGCGGGCACTGCGCCTGGCGTGTGTGACCCCCTCACAGGGCAGTGCTACTGTAAG
Seq A exon
GTGAGTGAGGGCTGGGCCCAGATCTGGCCTCTCCCTCCGGCCTCATCAGCTGAAAGTGTCCTTACGGGCCTTTCGGGGCAGCTGGGGCTTCCTAGAAGCTTTTGGGAGAGTCATCCCCATTGGCAGGTGGGTACCAGGAACCCGGGGTCAGGCACCTGGCACCTGCCGACCACTCTCACTGTCCTCTCATCCCTAG
Seq C2 exon
GAGAACGTGCAGGGCCCCAAATGTGACCAGTGCAGCCTTGGGACCTTCTCACTGGATGCTGCCAACCCCAAAGGTTGCACCCGCTGCTTCTGCTTTGGGGCCACGGAGCGCTGCCGGAGCTCGTCCTACACCCGCCAGGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000130702-LAMA5:NM_005560:36
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:
PF0005319=Laminin_EGF=PD(51.0=51.0),PF0005319=Laminin_EGF=PU(44.9=44.9)
A:
NA
C2:
PF0005319=Laminin_EGF=PD(51.0=53.2)
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:
CTGTGATACCTGCTCTCCGGG
R:
GGTGTAGGACGAGCTCCGG
Band lengths:
250-446
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)