HsaINT0090542 @ hg19
Intron Retention
Gene
ENSG00000050555 | LAMC3
Description
laminin, gamma 3 [Source:HGNC Symbol;Acc:6494]
Coordinates
chr9:133948017-133948708:+
Coord C1 exon
chr9:133948017-133948222
Coord A exon
chr9:133948223-133948631
Coord C2 exon
chr9:133948632-133948708
Length
409 bp
Sequences
Splice sites
5' ss Seq
CTGGTATCC
5' ss Score
2.3
3' ss Seq
TCTTCCTCTTCTTTCTACAGGAG
3' ss Score
11.94
Exon sequences
Seq C1 exon
GGGCTCGGGAAGCCTTCCTGGAGCAGATGATGAGCCTCGAGGGTGCTGTCAAGGCCGCCCGGGAGCAGCTGCAGAGGCTGAACAAGGGTGCCCGCTGTGCCCAGGCCGGATCCCAGAAGACCTGCACCCAGCTGGCAGACCTGGAGGCAGTGCTGGAGTCCTCGGAAGAGGAGATTCTGCATGCAGCTGCCATTCTCGCGTCTCTG
Seq A exon
GTATCCCAGGGGACCCCCCTACCCGAACACACCAAACCTGGGCATTGGTCCCTGCCCCAGCCCTCCCATTGACCTGGTGACCTTGGGTATGACTCCCCACTTTGGGAGGCTTAATTTCATCTGCAAAGTGGGGATCACACAGTGCCTCCTCCTGGATTCAGCGAGAGGATGTTTGCAAAGGGCGAGGCATGTTCCGAGGAGACTGAATGCGCAGTAAGTGGTGGGCTGCATCCTTATTGGTGTTTCTGCATCCTAGGACTCCGCTCACTGAATGCCGATGTTGTGGCCAGCTTTGTGCATTTATAAAACGACGGGTGCCATCCAGTTCTGCCTCACAATTGGACCAGATGTGGCCCTTACCCTTTGGCGATGGGCCATCAGTTTCCTCCTCTTCCTCTTCTTTCTACAG
Seq C2 exon
GAGATTCCTCAGGAAGGTCCCAGTCAGCCGACCAAATGGAGCCACCTGGCCACAGAGGCCCGTGCCCTCGCCAGGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000050555-LAMC3:NM_006059:19
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=0.538
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:
AAGCCTTCCTGGAGCAGATGA
R:
CCAGGTGGCTCCATTTGGTC
Band lengths:
246-655
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)