HsaINT0090333 @ hg19
Intron Retention
Gene
ENSG00000130702 | LAMA5
Description
laminin, alpha 5 [Source:HGNC Symbol;Acc:6485]
Coordinates
chr20:60893899-60894851:-
Coord C1 exon
chr20:60894740-60894851
Coord A exon
chr20:60894070-60894739
Coord C2 exon
chr20:60893899-60894069
Length
670 bp
Sequences
Splice sites
5' ss Seq
GCGGTAGGG
5' ss Score
6.22
3' ss Seq
GACGAACCCCTGCCCCACAGAGC
3' ss Score
5.76
Exon sequences
Seq C1 exon
GCCGTGGGGACCCGAGACCAGGCGAGCCAATTGCTGGCCGGCACCGAGGCCACACTGGGCCATGCGAAGACGCTGTTGGCGGCCATCCGGGCTGTGGACCGCACCCTGAGCG
Seq A exon
GTAGGGGCCAGCCCAGCCAGGCTCAGGGCTCAGAGCCAGGAGGGCTGCCTGGGGTAGGGGTGGGGGTGCCTGGCCGAGCTTGGCCTGGAAGAACAGGCAGGATCTGTCTTTTAGATGGGAGACGACGCCTCTGGAGTGAACAGTAGGGCAGGGTCAGGAGGTCGGCGACACAGCCGTGTGGCCAGACAGGTGGCCCCGGGAGACGTCAGACCCCTCGACAGCCTCCCCAGGAAATGTGCCGGTTAGATGTTCGCGCTCACAGATATCCCGTAGTGCACACTGAGACATGGGACTCAGGAGAGATTTGGCTCCCTGAGCCTGCCTAACAGGACCTGCCAGCCCAGCCTGGGGGTCGGCAGGGGGTGCCATGTCAGAGAGAGCTGGCCAGGGAGCAGGGTGGGCCAGGCGGAGAGGGGCAGGACGAGAAGGCTCAGAAGCTGGCTGAGCAGACTGGTGTCAGGGTGTTGGAGGCACTGCAGGAGGTGAGGGCCGGGCAGGTGAGGCAGCTGTGGCCTTTCGCCAGGTGCTCTAGGGGCCACCCAGGTGCGCTCAGGTTCCGGGCCCCTGGCCTGCCAAGGATGGCAGGGCTGGGGTCTTGGGCTTGGAAGCCAGCAGGCAGAGGTGCACTAGTACGGGCGGCCCCAGGCTCTGACGAACCCCTGCCCCACAG
Seq C2 exon
AGCTCATGTCCCAGACGGGCCACCTGGGGCTGGCCAATGCCTCGGCTCCATCAGGTGAGCAGCTGCTCCGGACACTGGCCGAGGTGGAGCGGCTGCTCTGGGAGATGCGGGCCCGGGACCTGGGGGCCCCGCAGGCAGCAGCTGAGGCTGAGTTGGCTGCAGCACAGAGAT
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000130702-LAMA5:NM_005560:51
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.105 A=NA C2=0.207
Domain overlap (PFAM):
C1:
PF060089=Laminin_I=FE(14.0=100),PF075866=HXXSHH=PU(0.7=2.6)
A:
NA
C2:
PF060089=Laminin_I=FE(21.5=100),PF075866=HXXSHH=FE(39.6=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GAGACCAGGCGAGCCAATTG
R:
ATCTCTGTGCTGCAGCCAAC
Band lengths:
270-940
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)