HsaINT0090377 @ hg19
Intron Retention
Gene
ENSG00000091136 | LAMB1
Description
laminin, beta 1 [Source:HGNC Symbol;Acc:6486]
Coordinates
chr7:107642003-107643416:-
Coord C1 exon
chr7:107643294-107643416
Coord A exon
chr7:107642179-107643293
Coord C2 exon
chr7:107642003-107642178
Length
1115 bp
Sequences
Splice sites
5' ss Seq
TAGGTAATT
5' ss Score
7.27
3' ss Seq
GTTGCCTGTCCTTCCCGCAGCCC
3' ss Score
10.64
Exon sequences
Seq C1 exon
AAAGGAAGACGGGAAGAAAGGGCAGGCGGCTCGGCGGGCGTCTTCTCCACTCCTCTGCCGCGTCCCCGTGGCTGCAGGGAGCCGGCATGGGGCTTCTCCAGTTGCTAGCTTTCAGTTTCTTAG
Seq A exon
GTAATTCCGTGGAAACGGTGCGGGGAGGCGGACGGACTTGGGCATGGGGAAGGAAAACCCAAAAGCTGCTTGCTCACCTTCGTGGGATCCTGGGGGCTTGGGAGAGGGACTGGATGGAAATGACGCCCCTGGGATTAAACGCCACCGCCCTTGCTTCGGTGGTGGCTGGAGACAGCGCACGCGGAGCGCCGCGGACCCTCATCCCCCGGGCTCTGCGCCCAAGCCCCGGCCCCTGCGGCCTCCCGCGGCCCCCGCTCAGGGTTTTGCACCCTCGGCCGGTTCACCCTGGGTTTCCCCACCGCAGAGGGCAGGTTCCCTGGGGTTGGCGGTGCTGACCGAGGAGGGCTCTCCAAAAATCCATTGCCCAGGAGAGTGCCTGAGCTGAGCGGAGGCTTCATTCTGGGAACAGATGGGGGCCATGTGGCTTTAATTAACCATCTCTGTTTGTCTCCGGATGGCACCAGAAACAGCAGGACCTGGCGCTTCCCTGGAATGGAGAAGCCTTGAAACCACTCCAGAGCCCCAGGGACTGTCCATGGGCTCCCCTAGCTCCGGAAAGCGGCGTCCACCGCGAGCCCCGGCGCCTCGTCCCCAGCGAAGCGCCGGTGACCCTCGCGCGTGCACGCACACGCACTCTCGCTTCCCAAGCTCACAGATCTCCACGCGCACACTCACACCGAGGATGCGCGGGCTGCCGCGTGCACGCGGGTTCACGTGCGTGGGTGTGTGGCCCTTTGGGGGTCAGCCTCCCTGCGCCGGGCTCCGGACACGTCGAAGTGGAGGGTCTACACATCCACCCTTTGTTGGGGGAGCTGCTCCCCGGGGCTGATCAGGGTGGGCGCGAGCGTCGGTGGGTTTCCCGGGAGGGAGGCTCTCGCTGCTGGACAGACCTGATGACGTGTGTGGGTTTCTTTCCGTGTCCTTCTCCTTTCGGAGTCCCTGCCTTCCCAGCCTCTCCTGCGCTCATCTCTCCATTGTCTTTTCTGTGCATTTTGCTTTCTTCCGAATGGACTGTCCTCTCTCCGCACCCACTCCCCCGCCCCCGCTTGTTCGTTTTTTTCGGGCTCCACTCCCTGCTTGTGTCCCCCCAACTCTGTTGCCTGTCCTTCCCGCAG
Seq C2 exon
CCCTGTGCAGAGCCCGAGTGCGCGCTCAGGAACCCGAGTTCAGCTACGGCTGCGCAGAAGGCAGCTGCTATCCCGCCACGGGCGACCTTCTCATCGGCCGAGCACAGAAGCTTTCGGTGACCTCGACGTGCGGGCTGCACAAGCCCGAACCCTACTGTATCGTCAGCCACTTGCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000091136-LAMB1:NM_002291:2
Average complexity
IR-C
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0005512=Laminin_N=PU(15.3=61.0)
Main Inclusion Isoform:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GAAGACGGGAAGAAAGGGCAG
R:
TGCAAGTGGCTGACGATACAG
Band lengths:
294-1409
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)