HsaINT0090315 @ hg19
Intron Retention
Gene
ENSG00000130702 | LAMA5
Description
laminin, alpha 5 [Source:HGNC Symbol;Acc:6485]
Coordinates
chr20:60902922-60903501:-
Coord C1 exon
chr20:60903297-60903501
Coord A exon
chr20:60903067-60903296
Coord C2 exon
chr20:60902922-60903066
Length
230 bp
Sequences
Splice sites
5' ss Seq
CAAGTGAGA
5' ss Score
5.26
3' ss Seq
AGCTCCCGCCCCTGCCACAGGTG
3' ss Score
6.94
Exon sequences
Seq C1 exon
CCTGTGACTGCGGTGCCCGCCTCTGTGACGAGCTCACGGGCCAGTGCATCTGCCCGCCACGCACCATCCCGCCCGACTGCCTGCTGTGCCAGCCCCAGACCTTTGGCTGCCACCCCCTGGTCGGCTGTGAGGAGTGTAACTGCTCAGGGCCCGGCATCCAGGAGCTCACAGACCCTACCTGTGACACAGACAGCGGCCAGTGCAA
Seq A exon
GTGAGAGCCCAGAGCGGCGTCAGCGCGGCCCCTGGTGGCCTTAAGGACAGCATTTCCTCTAGCCAGAGGGTCCTGGCACCCACCCTGCTCCCATTTGTGCTCCCTGGGTGCAGCAGCGCCCTCTCCTCCACTTCTGGGAGGATGCTGCCTGGGTGGGGGGTGCCTACGAGGTCTCACTTTGGTGTGAGTGACCTGGGGTGGAGGGGGCTCAGCTCCCGCCCCTGCCACAG
Seq C2 exon
GTGCAGACCCAACGTGACTGGGCGCCGCTGTGATACCTGCTCTCCGGGCTTCCATGGCTACCCCCGCTGCCGCCCCTGTGACTGTCACGAGGCGGGCACTGCGCCTGGCGTGTGTGACCCCCTCACAGGGCAGTGCTACTGTAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000130702-LAMA5:NM_005560:35
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(6.1=4.3),PF0005319=Laminin_EGF=PU(46.9=33.3)
A:
NA
C2:
PF0005319=Laminin_EGF=PD(51.0=51.0),PF0005319=Laminin_EGF=PU(44.9=44.9)
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:
CACGGGCCAGTGCATCTG
R:
TGAGGGGGTCACACACGC
Band lengths:
296-526
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)