HsaINT0090234 @ hg19
Intron Retention
Gene
ENSG00000053747 | LAMA3
Description
laminin, alpha 3 [Source:HGNC Symbol;Acc:6483]
Coordinates
chr18:21327907-21329510:+
Coord C1 exon
chr18:21327907-21328024
Coord A exon
chr18:21328025-21329391
Coord C2 exon
chr18:21329392-21329510
Length
1367 bp
Sequences
Splice sites
5' ss Seq
CTCGTAAGT
5' ss Score
9.63
3' ss Seq
TTAAAATATTTTCCTTCTAGATT
3' ss Score
8.95
Exon sequences
Seq C1 exon
CTCTTCCATGTGGCCTATATTTTAATCAAATTTGCAAATTCTCCTCGCCCTGATCTTTGGGTCTTGGAAAGATCTGTAGACTTTGGAAGCACCTACTCACCATGGCAATATTTTGCTC
Seq A exon
GTAAGTAATCTTGCCTACCATGTTATGCATGGCTTTAATTACTTGGAACAGATAAAGACTATGGATTTAATTAGAAAATTAATCTTGGCTGGGTGTGGTGGCTCACCCCTATAATCCCAGCATTTTGGAAGGCCAAGGCGGGTGGATTACCTGAGGTCAGGAGTTTGAGACCAGCCTGGCCAACATGGTGAAACCCTGTCTCTACTAAAAATACAAAAATTAGCCAGGCACATGCCTGTTATCCCAGCTACTCGGGAGGCTGAGGTCGGATTATCACTTGAACCCAGGAAGCAGATGTTGCAGTGAGCCAAGATTGTACCACTGCACTCCAGCCTGGGCAACAGGATGAGACTCTGTCTCAAAAAAAAAAAAAAAAGAAAAGAAAATTAATCTCTCAGTATGACTAGTTAGGGACTGGTCACTTTTAACCTCTAAATTACTCTCAGAACATTGACTGGGCGCGGTGGCTTATGCCTGTAATCCCAGCACTTTGGGAAGCCAAGGCAGGCGGGTCACTTGAGGTCAGGAGTTTGAGACCAGCCTGGCTAACATGGTGAAACCCTGTCTCTACTAAAAATACAAAAATAAGCAAAGTGTGGTGGTGTGCACCTGTGGTCCCAGCTACTCGGGAGGCTGAGGTGGGAGAATCACTTGAATCCAGGAGGCGGAGGTTGCAATGAGCCAAGACTGTGCCACAGCACTCCAGCCTGGGTGACAGAGTGAGACTCCATCTTGGAAAAAAAAAAAAAAAGAATATCCCCATTTTTCAAGCATGTGTTCAATAATTTCAAGGATACTACATGCAGAAATGAAGTAGAAACTCCTTTTATGATAACAGTTCTTGGCACTATTTGGGAGTACCTGTAAGATGGTAGAAGCTGTGAATTGATGAGATGACTTTAATAACTGTCATCTCCAATCTTTTCCCCTTTATGCAGAATTAGAAACTAAGTTCCATCTTTATAGTTCCTGTGCTGTGCTTTACTTACCTCAACTCTGTTATCTTCACTAATGAAGAATGTCAGGGTTTCTGAACCCTATGATGAACAGAGGTGGACAAGAATTTTGCTTATAAAGGCATTGGGTTTTCCACTAGGTTTCCTTAGAAGATAAACTTGCCTAAGTATGAGCGTGGAGTTAGCACTGCATCTCCAAGCATTGCCACTGAAAGTCAACTGGCCTGAAATGGCTTGGTATTTTCTTTCATGAATTAAAAACTCCATTATCAGCCTTTCTCTAAAAGTTTTAAATGCCTTTCTGTTTTTTCTTTCTTTGTGTATTTTCTTAAGGAAACATAAGGCTTCTTAAGAGATTTGCAACAAAATGATAATATTTTGTTTTATAATATTAAAATATTTTCCTTCTAG
Seq C2 exon
ATTCTAAAGTAGACTGTTTAAAAGAATTTGGGCGGGAGGCAAATATGGCTGTCACCCGGGATGATGATGTACTTTGTGTTACTGAATATTCCCGTATTGTACCTTTGGAAAATGGTGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000053747-LAMA3:NM_001127717:3
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:
PF0005512=Laminin_N=FE(15.5=100)
A:
NA
C2:
PF0005512=Laminin_N=FE(15.5=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CTTCCATGTGGCCTATATTTTAATCA
R:
CCATTTTCCAAAGGTACAATACGGG
Band lengths:
231-1598
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)