HsaINT0090211 @ hg19
Intron Retention
Gene
ENSG00000053747 | LAMA3
Description
laminin, alpha 3 [Source:HGNC Symbol;Acc:6483]
Coordinates
chr18:21478918-21479419:+
Coord C1 exon
chr18:21478918-21479029
Coord A exon
chr18:21479030-21479251
Coord C2 exon
chr18:21479252-21479419
Length
222 bp
Sequences
Splice sites
5' ss Seq
ACAGTAAGA
5' ss Score
5.96
3' ss Seq
GACCACTTGATGTTTCCTAGTTC
3' ss Score
4.75
Exon sequences
Seq C1 exon
GCTCAAGTAAATTCCAGAAAAGCACAAACATTAAACAACAATGTTAATCGGGCAACACAAAGCGCAAAAGAACTGGATGTGAAGATTAAAAATGTCATCCGGAATGTGCACA
Seq A exon
GTAAGAAGAGTTATTAAGCCCAATTACATTTTTTTTGGTTACATAACCTTCATTGTACACTAAAAGAATTCCCTTTAAGATTTCAACATTATGAAAAGAATCCCATAGTGATACTAAAAAACTAATATAAAATCTCCATAGAAGTTTCTACCTTTTTTTTTTTTTAAGTAGCCTACTGGAGCCCAGAATTCCCAGTCTAATAGACCACTTGATGTTTCCTAG
Seq C2 exon
TTCTTTTAAAGCAGATCTCTGGGACAGATGGAGAGGGAAACAACGTGCCTTCAGGTGACTTTTCCAGAGAGTGGGCTGAAGCCCAGCGCATGATGAGGGAACTGCGGAACAGGAACTTTGGAAAGCACCTCAGAGAAGCAGAAGCTGATAAAAGGGAGTCGCAGCTCT
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000053747-LAMA3:NM_000227:9
Average complexity
IR-C
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.579 A=NA C2=0.614
Domain overlap (PFAM):
C1:
PF060089=Laminin_I=FE(33.6=100),PF060089=Laminin_I=PU(1.0=2.6)
A:
NA
C2:
PF060089=Laminin_I=FE(21.0=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
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:
GCTCAAGTAAATTCCAGAAAAGCACA
R:
AGCTGCGACTCCCTTTTATCA
Band lengths:
278-500
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)