HsaINT0090226 @ hg19
Intron Retention
Gene
ENSG00000053747 | LAMA3
Description
laminin, alpha 3 [Source:HGNC Symbol;Acc:6483]
Coordinates
chr18:21406666-21407431:+
Coord C1 exon
chr18:21406666-21406763
Coord A exon
chr18:21406764-21407277
Coord C2 exon
chr18:21407278-21407431
Length
514 bp
Sequences
Splice sites
5' ss Seq
AAAGTCAGT
5' ss Score
1.98
3' ss Seq
TGTTGTTGCTGTTGTTGAAGTTG
3' ss Score
2.51
Exon sequences
Seq C1 exon
GATTACCTGGTGCTGCTCCCCAGGGACTACTATGAAGCCTCTGTACTGCAGCTGCCAGTCACAGAACCATGTGCCTACGCAGGACCTCCCCAAGAAAA
Seq A exon
GTCAGTGTGGGGCAGAAGGTGCAGCCGCATCATTGGGGTCCTCTAAATTAGGAGCCTTTAATGCAAGCTTTCATGAGGTGTCTCAGGATCACAACGACAGCATGATGCTCTGGATAATTAGTTGTTATCTTCCTCTATGTCTTACTTGTGTTCTTCAAGTAAGATTCACAAAGCACTTTGCACACCATAGCTGGCTTAGGAGTGGCTACCACCCTCCAGCATGTGGGAATGTTGATGCATGCCCAAGTCAATGCCCTCAAGGTCAGTCATACATCTGGTGGGAGGAAGAGCTTAAAATAGAAGCCAGGTTTGTGGACCTTTGTTTCTTCTCTTCCCCATGCAGATGAAAATTTATTGCTTAATTCTTGTAGCAGACACTTAATAAGAGTTTATTGAAGGATGATGAATGAATGAGTGAACTGAATGACTGAGAGTCTTTGGGGATGTACTTTGATATTCCGTTTGATGTTCTCAGTTGTAACTATTGATTCCATTGTTGTTGCTGTTGTTGAAG
Seq C2 exon
TTGCTTACTCTACCAGCATTTGCCAGTGACCAGATTCCCCTGTACCCTGGCTTGTGAGGCCAGACACTTCCTGCTTGATGGGGAGCCAAGACCCGTGGCAGTGAGGCAGCCCACACCTGCACACCCTGTCATGGTGGACCTCAGCGGGAGAGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000053747-LAMA3:NM_001127717:22
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=0.019
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
Associated events
Other assemblies
Conservation
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GATTACCTGGTGCTGCTCCC
R:
CTCTCTCCCGCTGAGGTCC
Band lengths:
252-766
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)