HsaINT0090305 @ hg38
Intron Retention
Gene
ENSG00000130702 | LAMA5
Description
laminin subunit alpha 5 [Source:HGNC Symbol;Acc:HGNC:6485]
Coordinates
chr20:62332557-62333243:-
Coord C1 exon
chr20:62333090-62333243
Coord A exon
chr20:62332718-62333089
Coord C2 exon
chr20:62332557-62332717
Length
372 bp
Sequences
Splice sites
5' ss Seq
GATGTGCGT
5' ss Score
4.37
3' ss Seq
TCACCCTGCCTTCCCTGCAGGTG
3' ss Score
13.23
Exon sequences
Seq C1 exon
CTGCCTCCTCTACACACACCTCCCCCTGGATGGCTTCCCCTCGGCCGCCGGGCTGGAGGCCCTGTGTCGCCAGGACAACAGCCTGCCCCGGCCCTGCCCCACGGAGCAGCTCAGCCCGTCGCACCCGCCACTGATCACCTGCACGGGCAGTGAT
Seq A exon
GTGCGTGTCCTGGGACCCCACGGAGCAATGGGTGTTGCAGGACCTTGGCCTGGGGGCTGGGGGTCCTGTGGCGGTGGCAGGTTATAGGAGCAGGGCGCTGCCTCAGGCAATGGAGCCCAGCACCCAGGCAGGGCGCCCCTGCCTCCTGCCTCCTGCCTCCTGCATGTGTGACCTCAGTGCCTGTCTGTATGTAGGATTGGCTGTGGCCTCCACATACAGCTCAGCCCCCACCACTTGCCTGGAGATGTCCGGGCCAGGGTGGGACTCGGCTGAAGGGCAGGCCCTGGGGTCAGGGAGGCGCTGGAGTGGGAGGGGAGGGAGGTGGGAAGGGCGAGGGGTGGCGGGCCTCCCGTCACCCTGCCTTCCCTGCAG
Seq C2 exon
GTGGACGTCCAGCTTCAAGTGGCAGTGCCACAGCCAGGCCGCTATGCCCTAGTGGTGGAGTACGCCAATGAGGATGCCCGCCAGGAGGTGGGCGTGGCCGTGCACACCCCACAGCGGGCCCCCCAGCAGGGGCTGCTCTCCCTGCACCCCTGCCTGTACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000130702:ENST00000252999:26
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.192 A=NA C2=0.153
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TGCCTCCTCTACACACACCTC
R:
CTGTACAGGCAGGGGTGCAG
Band lengths:
314-686
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