HsaINT0090519 @ hg19
Intron Retention
Gene
ENSG00000058085 | LAMC2
Description
laminin, gamma 2 [Source:HGNC Symbol;Acc:6493]
Coordinates
chr1:183205595-183206639:+
Coord C1 exon
chr1:183205595-183205739
Coord A exon
chr1:183205740-183206486
Coord C2 exon
chr1:183206487-183206639
Length
747 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGG
5' ss Score
10.07
3' ss Seq
TGGTTTCTTTGGGCTCATAGGTG
3' ss Score
7.18
Exon sequences
Seq C1 exon
ATTGGAGAAAACCAAGTCCCTGGCCCAGCAGTTGACAAGGGAGGCCACTCAAGCGGAAATTGAAGCAGATAGGTCTTATCAGCACAGTCTCCGCCTCCTGGATTCAGTGTCTCGGCTTCAGGGAGTCAGTGATCAGTCCTTTCAG
Seq A exon
GTGAGGGCATCTGGCCTGTGTGCTTGATATACAGGAGGGCCATAAATACTTTCTTTTCTGGGGGTGCCATAATATTGTTCAAACATTCAGCTTTTTCTCCATGTTGACCATTTCTGTTTTAGAGTGGGAAGAGTATTTAGCCTTCTCATTACCCATTTGCTTGTTCTTAAACCACAATCCTAGTCTCTGGAAAGGATTTGACCCATGCTAAACCTATTACTGGATAAAAGTTTTATGTATCTTCCTTAGTTCTGGGGATTGTTGAAACCTGTGGAAAATTTTTATAAAGTTTTTTTGTTTACGCTTGAGTCCAACCTATAGTATATCTCTATGTATAGCCACTCTGAGATGACTTCTTCTCAAAAGTTTTGCATTGTTTCTGCCATCAGTTCCTTTAACAATTCCAAACTTATTCGATTAAGAAGATTTTGTTTACTACCTATAGAAAAAAAAATTCACAATCCCCATGGATATATGTTCCCATGAATATATAAACTAACATGTAAACATTTAAAAAATGAAAAAGAACAGAGACAAAGCCTGTTTGACATTGAGGGGACCTGCTGCCTTACTTTCATTGGGCATACTGACTCATTTTTGTTAGGTTTTGGGCCTGGATGGCTAGTGACTATTTTCTTGGCTTCTTAAGGCTGTTGCTATTTTCAAACAATGGTGCCAGGTCCTAACAAGGCTGGTGTGGTAACTGGTAAGCAGAAGTCAGACTCCCTGGTTTCTTTGGGCTCATAG
Seq C2 exon
GTGGAAGAAGCAAAGAGGATCAAACAAAAAGCGGATTCACTCTCAAGCCTGGTAACCAGGCATATGGATGAGTTCAAGCGTACACAGAAGAATCTGGGAAACTGGAAAGAAGAAGCACAGCAGCTCTTACAGAATGGAAAAAGTGGGAGAGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000058085-LAMC2:NM_005562:17
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.306 A=NA C2=0.529
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GGAGAAAACCAAGTCCCTGGC
R:
TCTCTCCCACTTTTTCCATTCTGT
Band lengths:
294-1041
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)