HsaINT0090322 @ hg19
Intron Retention
Gene
ENSG00000130702 | LAMA5
Description
laminin, alpha 5 [Source:HGNC Symbol;Acc:6485]
Coordinates
chr20:60899497-60900602:-
Coord C1 exon
chr20:60900372-60900602
Coord A exon
chr20:60899611-60900371
Coord C2 exon
chr20:60899497-60899610
Length
761 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGG
5' ss Score
10.07
3' ss Seq
CTGCCCCCGTACACCCTCAGGAA
3' ss Score
7.04
Exon sequences
Seq C1 exon
GGGAACTTCCGGCATACGGAGACGCGCAACACTGTGTCCCGCGAGGAGCTCATGATGGTGCTGGCCAGCCTGGAGCAGCTGCAGATCCGTGCCCTCTTCTCACAGATCTCCTCGGCTGTCTTCCTGCGCAGGGTGGCACTGGAGGTGGCCAGCCCAGCAGGCCAGGGGGCCCTGGCCAGCAATGTGGAGCTGTGCCTGTGCCCCGCCAGCTACCGGGGGGACTCATGCCAG
Seq A exon
GTGAGGTTAGGACAGCACCAGACTGCGAGGCGGCTCACCTGTGCACACCCTTCCCTCCAGCATCCTCCCTGTGTTCCCTTCCTTGCTGCCTCCACTTCCTGTCACCCTACTCACCTCTCTTCCTGCCCCTGCTTTTCACAGGCTGCTGGCCAACTCATGGGCCTGCCTGTCCCCTGCTGCCTGTCTGCCTGCCCCTCGTCCGCCTGCCTGCCCCTCATCCGCCTGCCCCTCCATGCACACACCCTCCATACCCCTTTCCCACCTACCCCAGCCCCCACCACTGGGTCACCTGGACATCCCCCACCGACCATCCTGGCGTCTGCCTGTCATTCTGCCCATCCCTCGCCCACTGTGTGTCTGTCCAGCTGCTAATCTGCCCTGCTAATCTGTCTGTCTGCTGTAACTTTGCTCCTTCTGTATGAGGAGGTTTGTGGTTGAATACCTCCTAGAAGGAGTGGAAAGAGTAGGCCCTGGTCCACATGGAGTGGGTGGTCACCAGCCCCAAGGCCTGGTCATTCCCGAGACAGGACATCCGTGTGGCTTTGAGAGCTATGTCCTCAAACAGCAGCCAGGTGCTGGCCCACCTCCAGCCGGCCGAGGCCAGGAGTTCCTGACCAGCCTCTGACCCAGCGGTGACCATGCTCCACGGGTTCCCAGTGCCTCGTGCCTGCAGGATCCCTGAGGGTCTGACTTGTGAGCTTGCAGGGTGGGGCCCCTCGTCCTCTCAATCGCTGATGCCACCTGCCCCCGTACACCCTCAG
Seq C2 exon
GAATGTGCCCCCGGCTTCTATCGGGACGTCAAAGGTCTCTTCCTGGGCCGATGTGTCCCTTGTCAGTGCCATGGACACTCAGACCGCTGCCTCCCTGGCTCTGGCGTCTGTGTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000130702-LAMA5:NM_005560:41
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.013 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0005213=Laminin_B=PD(45.3=80.5),PF0005319=Laminin_EGF=PU(50.0=23.4)
A:
NA
C2:
PF0005319=Laminin_EGF=PD(44.4=42.1),PF0005319=Laminin_EGF=PU(36.2=44.7)
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:
GGGAACTTCCGGCATACG
R:
ACACAGACGCCAGAGCCAG
Band lengths:
344-1105
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)