HsaINT0090518 @ hg19
Intron Retention
Gene
ENSG00000058085 | LAMC2
Description
laminin, gamma 2 [Source:HGNC Symbol;Acc:6493]
Coordinates
chr1:183204710-183205739:+
Coord C1 exon
chr1:183204710-183204865
Coord A exon
chr1:183204866-183205594
Coord C2 exon
chr1:183205595-183205739
Length
729 bp
Sequences
Splice sites
5' ss Seq
AAAGTACGT
5' ss Score
7.99
3' ss Seq
CTCCCCACCCCCAACACCAGATT
3' ss Score
3.96
Exon sequences
Seq C1 exon
CCACGTTGAGTCAGCCAGTAACATGGAGCAACTGACAAGGGAAACTGAGGACTATTCCAAACAAGCCCTCTCACTGGTGCGCAAGGCCCTGCATGAAGGAGTCGGAAGCGGAAGCGGTAGCCCGGACGGTGCTGTGGTGCAAGGGCTTGTGGAAAA
Seq A exon
GTACGTTCCTACGGGTCCTCCCGTGGCTCATTATACCTTGGATACTCCCAGGGCAAAATGCTAACCGTACTTGAGGGGCACCATGCTAGTTGTAAAAAACATATTATTAATGATAATAAGAGGGCCGAAATCATGGGAGTTTTACTTTGGGGAAAAGCAGATATTTTTAAGACTGGAAGAAAAAAAGATTGGTTAGTCTAAATAAAATTAATGTTTTGATTGAGATTACAATACTGGGAGGTATGGTCACCCTCTGGTGTTTGAAGGGTGTGAATAAACCCATCTGATGGCATGGGGAGATATAAAAATACAGAAATATATTTCTGTTATCAAGAAGTGGGGAATTTGGGATTGAATTTTTCTGACCCAACCTGTGTAAATTAAAAGGCTTATGTTTAGTGGAGAGGGACAAGTATCTGATAAATAATTTTGTTTGGTTCTTCTGGTTATTCTAACTACATACTTTCAAGACAACAGGGTGAAATTTTGCTTTTGTTAAAAAAAAAGGGGGGGCCAGGTGTGGTGGCTCACTCTTGTAGTCCCAGCTACTTGGGAGGCTGAATTGGGAGGATTGCTTGAGCGTGGGAGGATGAGGCTATAGTGAGCTGTGATCACGCCACTGCACTCCAGCCTGGACAACAGAGTGAAACCCTGTCTCAAAAAAAAAAAAAAAAAAGAATTCTCAAAGTCCTCTTTTTATTACCGCCCCCTCCCCACCCCCAACACCAG
Seq C2 exon
ATTGGAGAAAACCAAGTCCCTGGCCCAGCAGTTGACAAGGGAGGCCACTCAAGCGGAAATTGAAGCAGATAGGTCTTATCAGCACAGTCTCCGCCTCCTGGATTCAGTGTCTCGGCTTCAGGGAGTCAGTGATCAGTCCTTTCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000058085-LAMC2:NM_005562:16
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.717 A=NA C2=0.306
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:
CCACGTTGAGTCAGCCAGTAA
R:
AGGACTGATCACTGACTCCCTG
Band lengths:
296-1025
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- 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)