HsaINT0090328 @ hg38
Intron Retention
Gene
ENSG00000130702 | LAMA5
Description
laminin subunit alpha 5 [Source:HGNC Symbol;Acc:HGNC:6485]
Coordinates
chr20:62322019-62322449:-
Coord C1 exon
chr20:62322269-62322449
Coord A exon
chr20:62322169-62322268
Coord C2 exon
chr20:62322019-62322168
Length
100 bp
Sequences
Splice sites
5' ss Seq
GGCGTGAGT
5' ss Score
7
3' ss Seq
ACCCAAGCCCCCCACCACAGGCT
3' ss Score
2.94
Exon sequences
Seq C1 exon
GAGGGACATTTTGGTTTCGATGGCTGCGGGGGCTGCCGCCCGTGTGCTTGTGGACCGGCCGCCGAGGGCTCCGAGTGCCACCCCCAGAGCGGACAGTGCCACTGCCGACCAGGGACCATGGGACCCCAGTGCCGCGAGTGTGCCCCTGGCTACTGGGGGCTCCCTGAGCAGGGCTGCAGGC
Seq A exon
GTGAGTGCTGGCCGGTCACAGGAGGGCGGATGGGGACTTCTGAGTGGGGTACGCTCCAAGGTCCCAGGCCAGCCATGCTCACCCAAGCCCCCCACCACAG
Seq C2 exon
GCTGCCAGTGCCCTGGGGGCCGCTGTGACCCTCACACGGGCCGCTGCAACTGCCCCCCGGGGCTCAGCGGGGAGCGCTGCGACACCTGCAGCCAGCAGCATCAGGTGCCTGTTCCAGGCGGGCCTGTGGGCCACAGCATCCACTGTGAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000130702:ENST00000252999:47
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.164 A=NA C2=0.039
Domain overlap (PFAM):
C1:
PF0005319=Laminin_EGF=PD(24.4=18.0),PF0005319=Laminin_EGF=PU(92.0=75.4)
A:
NA
C2:
PF0005319=Laminin_EGF=PD(6.0=5.9)
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:
CCCGTGTGCTTGTGGACC
R:
CACCTGATGCTGCTGGCTG
Band lengths:
250-350
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