HsaINT0090181 @ hg19
Intron Retention
Gene
ENSG00000053747 | LAMA3
Description
laminin, alpha 3 [Source:HGNC Symbol;Acc:6483]
Coordinates
chr18:21485486-21487630:+
Coord C1 exon
chr18:21485486-21485588
Coord A exon
chr18:21485589-21487513
Coord C2 exon
chr18:21487514-21487630
Length
1925 bp
Sequences
Splice sites
5' ss Seq
AAGGTATTA
5' ss Score
7.04
3' ss Seq
GATGCTTTATTTTATTTTAGAAG
3' ss Score
6.82
Exon sequences
Seq C1 exon
ACAGTGATAAAGGAAGATCTGCCAAGAAAAGCTAAAACCCTGAGTTCCAACAGTGATAAACTGTTAAATGAAGCCAAGATGACACAAAAGAAGCTAAAGCAAG
Seq A exon
GTATTAGGGGGAGTGGGCAATGGCAGGGATAGTCAGGAGCTTTAAATGACCTCTGGGACCAGGTGGGGCAGCCCTAGAAGCAAATGTTGTTTTTGAATCTCAGTGTCAATGCAGATGATACCCTTTATTTATTTTATTTTATTACTATTATTATTTTTAATAGAGATGGGGTCTCCGTTGCCCAGGCTGGAGTGCAGTGGCACAATCATAGCTCACTGTAGCTTTGAACTCCTGGGCTTAAGCTATCCTCCCACTTCAGCCTCCCAAGTAGCTGAGATTACAGGCGTGCACCACCATGCCCAGCTAATTTTTGTATTTTTTTTAGAGGCAAGGTCTTGCTATGTTTCCCAGGCTGGGCTCAAATTCCTGTCCTTACGGGATCCTCCTGTCTCAGCTTCCCAAAATGGTGGGATTACAAGCATGAGCCACCATGCCGGGCCCAGATAATACTTTTTAAATTCATGATTTATTTATCAATTTCATGTATCCACCCAATATTCTAAATATTCCCCACCTATCATGTACAAAATTAACTAGAGCCTTATAAATATAAATAAATCTTGAGAGTGATAGGCCTATTTGGGCCTGGCCTTGGTGGGGAGGCTATTTTAATTTAACCCACCTGTGATCATGGCATTGGCAACCCCACATGTCAAGATCATTGGTTTGGGATCATTAGAATAACTGCTTTAAAATTTCTTAAGTCCTAAAATCTTTGCAACTAAAAGTCCCCAAAATCACTGCTACTGTGAAGCATGAGAATTTTTTAAGCATAAATTTTATCTCTGGAAAATTTTCATGTATTTTACTTACTTATTTTTTTAAATAATTAAACTCTCTCAATCTCACCAAATTTCTGTGTTTGAAAAATGCTGTTTCTTGTGTTTCTCCAGGCTCTTGTTGTCATCCATGAGTCCAAGGCCCTCATTCAGCCTCTTAGTCCTTTCAGAGGGATTAAATGATGCCTCTGTAAATTAAATAATTTCTCTCCTTTCTGCTTCCTTCTTTTCCTTCCTTCTTTCTTTCTCTCTTTCCTTCACATGTTAAAAAATTAAAGACATGAAAAATAAAATACCAAAAAAGTACTAACATACAATCATTTGCCTTGCAAATTTCAATAATTTGGATTTCCTGGTATGACATCTATTTCTCTCTACAAAATTTGAGCTTCGAGGTAGGCTCAGTGTGCTAAACAGGGTTAGGATGCTAACTATGTTGCTATGTAAACCAGTCCTGGAATCGTAATTGAAGCCATGAATCATCAAGATGGTCTTAAAGCATTTGCTGGTCATTTTTGATGACCCAAGGATGGCAATATTATCAGCTAGGAATGTCTGCTAGCTCCCTTTCTTTCACAGAATTTTTAAAATGTGTCATTTTGGAAATTAACAGAAACAAACAGTGCCTACTTTGTGTCTGTATTTGCCTGGATGAGGCTCTTTCAACAACACTCTTTTCTTGTCCTCTGATGGAAGAGGATCCTTTCTACATTATTAATTCATTCATTCACTCATGTATTCATTTACTCAACAAACATATACTAATATTACGCCTCAACTAGTGCCAGACACTACATTATGTGGTAGGACATGGTAGTGGATAAGACAGATGCATCTTTTACTAAACAGAGTCTCTTACTCTGAGCAGTTAAGAAGTTTAGCCTTCCCCAAGTTATTCAGCCTCTTTCTTTCTTCCTGTGTATTTCCAAGGCATTACCACAAGGCTCTGATTTGCTGCTGACCTCTGTAACTGGAGGATCCCAGAGCTGTGGGTCTGGGCACATGCAGTGGGCATCTCTGAGGTGACCCCTAAGAAGCAAGTCTACTCAATGCTGTGCAGACACTGGCTACTTCAGGGGCCACAAATACCAATGGAGGATCAAAATGCACAAAGTAATTGCCTCCTGATGCTTTATTTTATTTTAG
Seq C2 exon
AAGTCAGTCCAGCTCTCAACAACCTACAGCAAACCCTGAATATTGTGACAGTTCAGAAAGAAGTGATAGACACCAATCTCACAACTCTCCGAGATGGTCTTCATGGGATACAGAGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000053747-LAMA3:NM_000227:15
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.657 A=NA C2=0.100
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
Associated events
Conservation
Rat
(rn6)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
ACAGTGATAAAGGAAGATCTGCCA
R:
GTATCCCATGAAGACCATCTCGG
Band lengths:
214-2139
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- 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)