HsaINT0090182 @ hg19
Intron Retention
Gene
ENSG00000053747 | LAMA3
Description
laminin, alpha 3 [Source:HGNC Symbol;Acc:6483]
Coordinates
chr18:21487514-21487899:+
Coord C1 exon
chr18:21487514-21487630
Coord A exon
chr18:21487631-21487719
Coord C2 exon
chr18:21487720-21487899
Length
89 bp
Sequences
Splice sites
5' ss Seq
GAGGTCAGC
5' ss Score
5.66
3' ss Seq
CCTATCTGTGTGTGCATTAGGTG
3' ss Score
7.92
Exon sequences
Seq C1 exon
AAGTCAGTCCAGCTCTCAACAACCTACAGCAAACCCTGAATATTGTGACAGTTCAGAAAGAAGTGATAGACACCAATCTCACAACTCTCCGAGATGGTCTTCATGGGATACAGAGAG
Seq A exon
GTCAGCATCTTCCTAATCCATTGTACTCGGTTGGCTTCTTTTGTTGAACGTTTTAGATACTTATACCTCCCTATCTGTGTGTGCATTAG
Seq C2 exon
GTGATATTGATGCTATGATCAGTAGTGCAAAGAGCATGGTCAGAAAGGCCAACGACATCACAGATGAGGTTCTGGATGGGCTCAACCCCATCCAGACAGATGTGGAAAGAATTAAGGACACCTATGGGAGGACACAGAACGAAGACTTCAAAAAGGCTCTGACTGATGCAGATAACTCGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000053747-LAMA3:NM_000227:16
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.100 A=NA C2=0.295
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF060097=Laminin_II=PU(39.5=83.6)
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:
TCCGAGATGGTCTTCATGGGA
R:
TCTTCGTTCTGTGTCCTCCCA
Band lengths:
175-264
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)