HsaINT0090485 @ hg38
Intron Retention
Gene
ENSG00000135862 | LAMC1
Description
laminin subunit gamma 1 [Source:HGNC Symbol;Acc:HGNC:6492]
Coordinates
chr1:183117534-183118146:+
Coord C1 exon
chr1:183117534-183117723
Coord A exon
chr1:183117724-183118033
Coord C2 exon
chr1:183118034-183118146
Length
310 bp
Sequences
Splice sites
5' ss Seq
CAGGTAAGA
5' ss Score
10.77
3' ss Seq
GGCCCTTTCTTTCTCTCCAGGCT
3' ss Score
10.97
Exon sequences
Seq C1 exon
CAAAGTTCTTGGGCAAGCAGGTGTTGAGTTATGGTCAGAACCTCTCCTTCTCCTTTCGAGTGGACAGGCGAGATACTCGCCTCTCTGCAGAAGACCTTGTGCTTGAGGGAGCTGGCTTAAGAGTATCTGTACCCTTGATCGCTCAGGGCAATTCCTATCCAAGTGAGACCACTGTGAAGTATGTCTTCAG
Seq A exon
GTAAGATAGCCTTCTTTGTAAAGTGAGACTTGACGAACATTGTGAAAGTGGTGTCTTTATTTAAGTTTAACTGGCCTCTAGATGTATTTTAAAGAAAAACTTCTGGGTTATTGTGGTGATTTTGTAAAAGGGAGCCTTCCTTTCTTTACCTTTATCTTTTCCAATTGTACTACCAAACCAATAGTCTTATTTTTTATTTGATTTGATTGTTAGAGCATTGCATTGTTGGGGCATAAATGAATAAGAAATATTTCCCCAACATCCAGAATTGTCCTTACAGAGGTTAATGTGGCCCTTTCTTTCTCTCCAG
Seq C2 exon
GCTCCATGAAGCAACAGATTACCCTTGGAGGCCTGCTCTTACCCCTTTTGAATTTCAGAAGCTCCTAAACAACTTGACCTCTATCAAGATACGTGGGACATACAGTGAGAGAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000135862:ENST00000258341:10
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0005213=Laminin_B=FE(48.1=100)
A:
NA
C2:
PF0005213=Laminin_B=FE(29.0=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CAAAGTTCTTGGGCAAGCAGG
R:
TCTCTCACTGTATGTCCCACGT
Band lengths:
302-612
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