HsaINT0090546 @ hg19
Intron Retention
Gene
ENSG00000050555 | LAMC3
Description
laminin, gamma 3 [Source:HGNC Symbol;Acc:6494]
Coordinates
chr9:133952574-133954685:+
Coord C1 exon
chr9:133952574-133952721
Coord A exon
chr9:133952722-133954535
Coord C2 exon
chr9:133954536-133954685
Length
1814 bp
Sequences
Splice sites
5' ss Seq
CTGGTCAGC
5' ss Score
3.85
3' ss Seq
AGCGCATTGTCTCCCTGCAGCCT
3' ss Score
8.5
Exon sequences
Seq C1 exon
GTACCAGGAGGTCCAGGCGGCCCAGAAAGCACTGAGGACGGCTGTGGCAGAGGTGCTGCCTGAAGCGGAAAGCGTGTTGGCCACCGTGCAGCAAGTTGGCGCAGATACAGCCCCGTACCTGGCCTTGCTGGCTTCCCCGGGAGCTCTG
Seq A exon
GTCAGCTCAGTTGTCTCAGAGCTCCGTGTGGGGTCGGGAGGATCTATTATAGAAGCTGGAGGCTGGGCACGGTGGCTCACGCCTGTAATCGCAGCACTTTGGGAGGCCGAGGCGGGTGGATCACCTGAGGTCAGGAGTTTGAGACCACCTGGGCCAACGTAGTGAAACCTAGTCTCTACTAAAAATACAAAAATTAGCCAGGTGTGGTGGTGCGTGCCTGTAACCCCAGCTACTGGAGAGGCTAAGGCAGAAGAATCACTTGAACCTGGGAGGCAGAGGCTGCAGTGAGCCAAGATTGCACCTCTGCACTCCAGCCTGGGCGACAGAGCAAGACTCCATCTCAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACTATTATAGCAGCTGGAGAAACCGGTGGGGCCCAGGCAGAGGCAGGTGATATGGCTCATTTTTAACTATATTGCAGCTAAGTCAAATGATATAACCTACCTATGGGGCTTGGCAGAGTCAGAGCTCAACCATTTCAACCATTCTCTGTTGATAATGTTAAGGCTGGGGCCTCTTCCTCCTTACAGTGACATTAGCAGTGTCATCAGATGGACACGGGATGCAATCCCAGCTCTGCCACTCCAGCTCTGTGACCTCGGCCAAGGACTTTCCCTTCCTGAGCCTCAGTCTGTCACATAGAACTCACCCATTAGGTTATTTCGAGGCTGCTTCCATGGGAGCTGGACAGAGATTCGGGAGCAATGCACGAGGTAGCTGGCCGACCCCTCTGTGCTCATCGCCTTATACTCATCACCTCTGCATGAACCGGGTCCATCGTGTCGATTCAGTAACCCTGAAATCCCAAAACTCAGAAACTGAACATTAAAGAACTCAGCTTGGCCGGGCGCGGTGGCTCACACCTGTAATCCTAGCACTTTGGGAGGCTGAGGCGGGCGGATCACGAGATCAGGAGATCGAGACCATCCTGGCTAACATGGTGAAACCCCATCTCTACTAAAAATACAAAAAAATTAGCCAGGCATGGTGGCGGGCGTCTGTAGTCCCAACTACTCGGGAGGCTGAGAATGGCATGAACCTGGGAGGCGGAGCTTGCAGTAAGCTGAGATTGCGCCACTGCACTCCAGCCTAGGTGACAGAGTGAGATTCTGTCTCAAAACAAAACAAAACAAAACAAAAAAAACTCAGCTTATAAAAATGCATTTGGGACAAGTGCTAACCCAGATTGATGCCCAAGGCTGCTTATTTGAGATCTTTGCTCCTCCCACTGCGTGCGGAGAGTAATGCACAGCTGTTAGTGTGTTTGAGCCCAGGTTCTGCTTCCAGCACCACTCAGGGTGTTAGGTCATAGGTAGAACCTGCACAGTTCTCCTATAAGTCTGGGAAATTCTGCATTCGGAAGCCATCCAGCCCCCAGATCTCAGTTCAGGGCTGTGGAGCTGGGGAAGCATTCCCACTTTGCAGTGGGGCAGTGTGGGTCAGGGAGGTTAGCTGGGTTGCTCAAGGCCACGCAGCTAGAAATTGGTAGGACTGTCATCTGAGCCCCAAGTAAGGGCTTCCCCAGCCTGGCTCCTCTCGCCCTGGGCCCTCTGCCTCCAGGGGTCCACACAAAGCCTGACCCCTGCTATTCCTGCCTCTGGGCTTCCGAGCTACCTGGGGCATCAGCTAGGCTCACCAGGTTTTCAGGGGGCTTGGGTTCTTGGCTGGCAGCCAGGGGCAGACCCGCCGCCTCAGCCCAGCAGGGCACCTCCCCCAAGGAGAGGATCCGCTGCTTGCCCTTCCTTTCCAGGCCCTGCCTGAGCGCATTGTCTCCCTGCAG
Seq C2 exon
CCTCAGAAGTCCCGGGCTGAAGACCTGGGCCTGAAGGCGAAGGCCCTGGAGAAGACAGTTGCATCATGGCAGCACATGGCCACTGAGGCTGCCCGAACCCTCCAGACTGCTGCCCAGGCGACGCTACGGCAAACAGAACCCCTCACAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000050555-LAMC3:NM_006059:22
Average complexity
IR-C
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.013 A=NA C2=0.423
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GTCCAGGCGGCCCAGAAA
R:
TTGTGAGGGGTTCTGTTTGCC
Band lengths:
286-2100
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)