HsaINT0090299 @ hg19
Intron Retention
Gene
ENSG00000130702 | LAMA5
Description
laminin, alpha 5 [Source:HGNC Symbol;Acc:6485]
Coordinates
chr20:60909578-60910182:-
Coord C1 exon
chr20:60910077-60910182
Coord A exon
chr20:60909678-60910076
Coord C2 exon
chr20:60909578-60909677
Length
399 bp
Sequences
Splice sites
5' ss Seq
GCAGTGAGT
5' ss Score
7.39
3' ss Seq
CTCCCACCTTCTCCCTGCAGGCT
3' ss Score
12.63
Exon sequences
Seq C1 exon
GGCACCGGCCAGTGCTTCTGCAAGCCCCACGTGTGCGGCCAGGCCTGCGCGTCCTGCAAGGATGGCTTCTTTGGACTGGATCAGGCTGACTATTTTGGCTGCCGCA
Seq A exon
GTGAGTGCCCACTCGCTCGTCCCAGACCACAGCCCTGCCTCCCCTCGGTTTATGCTGGGGAACCCAAGGCCCGGAGGGACAAGTGCAGCCTGGGCAGCATGAAGCCCGGGTGATGGATGGCTGCCCCTTGGTGCCAGCCTGTGCCAGGGTGTGGGAGAGGGGGTGCAGCTCCCACCCAGATGCGTGGCTTCCTCTCCCCTGTCCTACACCTGGGCAGACGGCACTAACAGATCCCAGCGCCCTCACCCTCGCCCTCGCCCTCGCCCTGAGCCCTGAGCCCTGAGCCCTGACTCTCCATCATCCAGAGAGCCCCAGGCAGGCTTCTCAGTCTGGCTGTGAGGGGCCCCTGAGGCTGGGTGGGGGCCAGGCAGCCTCTGACCTCCCACCTTCTCCCTGCAG
Seq C2 exon
GCTGCCGGTGTGACATTGGCGGTGCACTGGGCCAGAGCTGTGAACCGAGGACGGGCGTCTGCCGGTGCCGCCCCAACACCCAGGGCCCCACCTGCAGCGA
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000130702-LAMA5:NM_005560:20
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(64.7=91.7)
A:
NA
C2:
PF0005319=Laminin_EGF=PU(72.7=94.1)
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:
CACCGGCCAGTGCTTCTG
R:
GTGGGGCCCTGGGTGTTG
Band lengths:
195-594
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)