HsaINT0090549 @ hg19
Intron Retention
Gene
ENSG00000050555 | LAMC3
Description
laminin, gamma 3 [Source:HGNC Symbol;Acc:6494]
Coordinates
chr9:133960911-133963009:+
Coord C1 exon
chr9:133960911-133961110
Coord A exon
chr9:133961111-133962862
Coord C2 exon
chr9:133962863-133963009
Length
1752 bp
Sequences
Splice sites
5' ss Seq
AAGGTCAGG
5' ss Score
6.23
3' ss Seq
CACTGCCACCCATCCCATAGCTT
3' ss Score
6.19
Exon sequences
Seq C1 exon
GAATGAAGCTGCAGTTTCCCCGGCCCAAGGACCAGGCGGCATTGCAGAGGAAGGCAGACTCCGTCAGTGACAGACTCCTTGCAGACACGAGAAAGAAGACCAAGCAGGCGGAGAGGATGCTGGGAAACGCGGCCCCTCTTTCCTCCAGTGCCAAGAAGAAGGGCAGAGAAGCAGAGGTGTTGGCCAAGGACAGTGCCAAG
Seq A exon
GTCAGGGTGGTGGCTGTGACAACAGTGGCCTCCTTCCCTCCCGGGGGGACCGCCCTTCCGCGGGCCCCTTCCCGACATCCGTGCTGACTACTCCGCACTCACTCACTGCTCAGTGGGCCCAGGCAATTAGCTCAGAGACTTCACGGGGGTGAGTCTGTGGGTTCCTCACGAAATAGGTGTCATTGCTGTCCCCATTGTACAGGTGAGAATGCTGAGGTGCAGCCAGCTTCATGAACTTAACCAGGACTTACACCTGGGTCTGCTGGCTTTCCTGCCTAAACTTCTAGGTTTTTCTTTTCTTTTTTGTTATTTTGAAGTTTGCGTTTATTTATTTTACCTGCCTTTTTGTTTTCAATTTTTTTCTTAATTTTTTCAGACAGATTCTTACTCTGTGGCCCAGGCTGGAGTGCAGTGGCGCAATCTCAGCTCACTGCAATCTCCGCCTCCTGGGTTCAAGTGACTCTCCTGCCTCAGATTCCAGAGTGGCTGGGATTATAGGCGTGCTCCACCACACCTGGCTAATTTTTGTATTTTTAGTAGAGCGGGGTTTCACCATGTTGGCCAGGCTGGTCTCGAACTTCTGATCTCAGATGATCCACCTACCTTGGCCTCCCAAAGTGCTGGGATTACAGGTGTGAGCCACTGCACCCAGCTTAAGGGTTTTTGGTTTTGTTTTTTTTTTTTGCTTGTTTGTTTGTTTTTTGTAGAGACAGGGTCTCTGTCGCCCAGGCTGGAGTACAGTAGCACAATCACAGCTCACTGCAGCCTCAAACCCTTGGGCTTAAGTGATCTTCCTGCCTCAGCCTCCTGAGTAACTGGGACTACAGGTGTGTGCCACTGTGCCTGGCTAACTTTTTTTTTTTTGCAGAGATGAGGAGTCTCGGCCAGGTGTGGTGGCTAACTCCTGTAATCCCAGCACTTTGGGAGGCCAAGGCAGGCAGATCACTTGAGGTCAGGAGTTCGAGACCAGTCTGGTCAACATGGTGAAACCCTGTCTCTACTAAAAATACAAAAAAATTAGCCGGGCATGGTGGCTCGCACCTGTAGTCCTAACTACTCCAGAGGCTGAGACACAAGAATTGCTTGAACCTGGGAGGTGGAGGTTGCAGTCAGCCAAACTGCACCACTGCACTCCAGCCTGGGCAACAGAGGGAGACTCTGCCTCGAAAAAAAAAAAGAAAAAAAAGATTGGGGTCTCACTATGTTGCCCAGGCTGGTCTTGAACCTCTGGTCTCAAGCAAGCCTCCTGCCTCAGCCTCCCAAAGTGCTGGGACCATAGGCATGAGCCACTGCACCCAGCCCTGGCTGATTTTAACTAGGCTTTTAAAAAATTGGTGCCAAATTCTAATCAGTGCCTATCTCCCCAGCTCTGCTGCTGGTTCTGTTGCTCACACACCAAGGAAACTGTCTTTATGGTGCCTAGGAAAAGTGCTGGGTTTGCAGTAGGGGTCCCCGGGCTTGATCTCTTGTCATGCCCCTCGGGCTTTGGCCAGCCCCTCCTCCCCTCTGTGCCTCTGTTTCCTCACCTGTAAAATAGTTAGAATTGCTCCTCCTGAAACGGGTGGTATCCAGCAGTCTACACTGTGCCCAGCACTTAGCCTGCATTCAGTACATATTTGTTGCGTGCATGAATGAATGAATGATCTGCCTGGTACAGACAACTGCTTGGCATCATTGCCATAAGAGCTATTTACCTCCAAAAGGACTTGCTGCACTCACTTCTTCTCCCTGCCACTGCCACCCATCCCATAG
Seq C2 exon
CTTGCCAAGGCCTTGCTGAGGGAGCGGAAACAGGCGCACCGCCGTGCCAGCAGGCTCACCAGCCAGACGCAAGCCACGCTCCAACAGGCGTCCCAGCAGGTGCTGGCGTCTGAAGCACGCAGACAGGAGCTGGAGGAAGCTGAGCGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000050555-LAMC3:NM_006059:25
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.891 A=NA C2=0.831
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AATGAAGCTGCAGTTTCCCCG
R:
CGCTCAGCTTCCTCCAGC
Band lengths:
345-2097
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)