HsaINT0090509 @ hg19
Intron Retention
Gene
ENSG00000135862 | LAMC1
Description
laminin, gamma 1 (formerly LAMB2) [Source:HGNC Symbol;Acc:6492]
Coordinates
chr1:183085902-183086577:+
Coord C1 exon
chr1:183085902-183086038
Coord A exon
chr1:183086039-183086454
Coord C2 exon
chr1:183086455-183086577
Length
416 bp
Sequences
Splice sites
5' ss Seq
TTGGTAATT
5' ss Score
5.73
3' ss Seq
TTTTCCTTCTCTACCTGCAGATG
3' ss Score
13.74
Exon sequences
Seq C1 exon
ATGCAAACCTGGATTTTTTAATCTGGAATCATCTAATCCTCGGGGTTGCACACCCTGCTTCTGCTTTGGGCATTCTTCTGTCTGTACAAACGCTGTTGGCTACAGTGTTTATTCTATCTCCTCTACCTTTCAGATTG
Seq A exon
GTAATTTAGACCTCATCCCCCAACCTGTTAGAACTGTGAGATTACACTTAAAATATTTTTAAAAATAAAATCAGTGACTCTTTGAGGGCTTTTTGATGGTTGGCAACACTTTGTATTATTTAGCATGCATAGTTTTTGTAGTTTGGCCTTTTAATTTAATGAAAATGTACTTTTGGCTTTAGAATTTATCTCAATGAATGGTGATTACAAATGTTATATAAATAGTAATAAAGTAAAATATAGTTTGAGTGGTATAGCATATATTGGTACTGTTGTAGGATCCATTTATTCAAAAAGGTTTATTGATGCCTTTCTGTATACAAGGTGTGGTCTTACACATTTTTATGATACATAGAGGACCTGAATTCAGGATGTTTACAGTGTAAAGTGCTTGTGTTTTCCTTCTCTACCTGCAG
Seq C2 exon
ATGAGGATGGGTGGCGTGCGGAACAGAGAGATGGCTCTGAAGCATCTCTCGAGTGGTCCTCTGAGAGGCAAGATATCGCCGTGATCTCAGACAGCTACTTTCCTCGGTACTTCATTGCTCCTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000135862-LAMC1:NM_002293:8
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=0.000
Domain overlap (PFAM):
C1:
PF0005319=Laminin_EGF=PD(33.3=34.0)
A:
NA
C2:
PF0005213=Laminin_B=PU(3.8=11.9)
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:
CTGGAATCATCTAATCCTCGGGG
R:
CAGGAGCAATGAAGTACCGAGG
Band lengths:
238-654
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
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)