HsaINT0090203 @ hg19
Intron Retention
Gene
ENSG00000053747 | LAMA3
Description
laminin, alpha 3 [Source:HGNC Symbol;Acc:6483]
Coordinates
chr18:21529993-21531741:+
Coord C1 exon
chr18:21529993-21530123
Coord A exon
chr18:21530124-21531647
Coord C2 exon
chr18:21531648-21531741
Length
1524 bp
Sequences
Splice sites
5' ss Seq
AAGGTGTGT
5' ss Score
6.64
3' ss Seq
AAAATGCATGTGTGTTCCAGGTC
3' ss Score
7.37
Exon sequences
Seq C1 exon
CTCACTCTGTATTGTTGGGGCCAGAATTTAAGCTTGTTTTCAGCATCCGCCCAAGAAGTCTCACTGGGATCCTAATACACATCGGAAGTCAGCCCGGGAAGCACTTATGTGTTTACCTGGAGGCAGGAAAG
Seq A exon
GTGTGTAGCAGTCTGATGCCATGGGGAGGGTCTGTAGAAACCAGCTTCAATGTCTGGAGGCCACAGCGGGTCAGGTTTGTAGTAGAGAATGGGATCCAATCTTGTATTTAAGAGCCTTGACTTCAGTGCTAACTTACCATTTTCCTTTAGCAAGTAATTTTATCATCATGTTTTCTGTTCTTAATTTTTAAAACTGGGAAAACTCAAACAAGTCGGGCTGAATTGCAGGTCCAGCACTTGGTTATATGGTCCTAAGGATGTTACTCAAGCTCTTTCAGACTTATCTGTAAAATGTAGATAATAACTCTTATAACTTAAGGCTTTTGTCAAGATTATAGAAATCGCCATATACTCAATTCTTACAGATTCTTTCTTCATCTCTGCAGCCTCATTTTTCCATCACTCACAGGCCTGAGTCAACATCTTATTTTCCACCACCCAGTTATATCTCTTTCCTTCTCAAAGATGTCTCTTTAAAACCAGATTCTTCTAGGAAGACCCTTAGTTGAGGCCTCGAGTGAAAGATTGATATAATATGCCATTTTCTTTCATCTCCGTCCTTCCACAGTTTACTAAATGTGAGGGGAAAAGAATCCCAGAAGAAAATAAAATGCCCAAAATTCCTAGAATACTTTCTATTGTAGTCTTTAATTAAGTCTGAGTAGGTCTCTGGTAGCCCAGAAAAGCAAGTAACTATCCACTTGCAAGGTGGTTGAGACAATTCTGGTTTTTCAGAGGAGGAGCTGGAGAGAGTCTCTACTGAGAGTCTCTGGGAGGGAATTATTCTCAGGAAAACAAATCAAGACCCGATGACCTTCATAATAGCAGTGACATTGTTTAGCTCAAAAATTGCCTGTGAATAGGCTGTCCCATCTAGCTACATGCAAATTAAATGTAAATTATTTATAAACACACTTATTTTAGTCCTCTCATTTCATTCCCCTTGATTCAACTCTTGGAAGATCCTGGAGGAGACCCTGATTTAGAAAGCAGGAATGTGGGATTCTGCACAAAACAGACTGCGTGCCTGGCTCCCGATGCGTGCCCAGAGCAAACTCAATCATTTTGCTTGTTTAAAGTCTTGCCATGCATGGAACTATTACAGTTGGCTGGCCCTTGCAGCAGGCTGTAGGCCTCCACCAGTAGCTTTGCCTTCCACATCTCACATATCCTTCCATACAGAGCCACTGTCACGCATTAATTGCTAAGGAGGATTCCAATCAGTAACCTTTGAGTTGAGCTGATGGGGGCGGGGTTTGGATTAGAAGGGAACAACTCATTGCCATTGGCAACGACTTCAGGCCAGGGTCCACCCTGGTTTATAGTTGCCTGGAAGGGATGCAGCAGAGAGATCTCTGGAAGCATTGGACCCCATGTGGTCAAATGCTTCAAAAGCGGAGGAGGGCCAATATCTAATGTGCCCTTAAGCTGTCAGTTGGCCCGGTTTGGGGAGGGAAGATGGCAGGGGAAGGTCGGCTCCACCTGCCTTCCTGAAGGAAATAGGAAAATGCATGTGTGTTCCAG
Seq C2 exon
GTCACGGCCTCTATGGACAGTGGGGCAGGTGGGACCTCAACGTCGGTCACACCAAAGCAGTCTCTGTGTGATGGACAGTGGCACTCGGTGGCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000053747-LAMA3:NM_000227:35
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=0.281
Domain overlap (PFAM):
C1:
PF0221019=Laminin_G_2=PU(22.2=63.6)
A:
NA
C2:
PF0221019=Laminin_G_2=FE(24.6=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
Associated events
Conservation
Rat
(rn6)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CTCACTCTGTATTGTTGGGGCC
R:
CCACCGAGTGCCACTGTC
Band lengths:
222-1746
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- 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)