HsaINT0090199 @ hg19
Intron Retention
Gene
ENSG00000053747 | LAMA3
Description
laminin, alpha 3 [Source:HGNC Symbol;Acc:6483]
Coordinates
chr18:21519187-21523935:+
Coord C1 exon
chr18:21519187-21519350
Coord A exon
chr18:21519351-21523751
Coord C2 exon
chr18:21523752-21523935
Length
4401 bp
Sequences
Splice sites
5' ss Seq
CAGGTATTA
5' ss Score
7.26
3' ss Seq
ATCGCCGATGTTCCCAACAGGTC
3' ss Score
9.17
Exon sequences
Seq C1 exon
CTGTTGCAGGACACACCAGTGGCCTCCCCAAGGAGCGTGAAGGTGTGGCAAGATGCTTGCTCACCACTTCCCAAGACCCAGGCCAATCATGGAGCCCTCCAGTTTGGGGACATTCCCACCAGCCACTTGCTATTCAAGCTTCCTCAGGAGCTGCTGAAACCCAG
Seq A exon
GTATTATTTAGCTTTCCTGCCCCAGCACCAGCTCAGAACCTGACTCTGCGATTCCACCTCAGGGAAGTCTGACTGCCATGACACCATGCAGCTCTCTCTAATGAAGGTGGCACTACCATTTTTGTGCAAAGAGGTGCTGGCCTGCACAGGACAGGGAGCGTGATTGCCTGCCATGTGCTTTCCCAACAGCTGGAGGCAAACGTGACGACAGTGTACTTCTCAGAGGCTGAAACAATCAGCTCAGGTCTGGTTTAGAATTGATGGTGTTCTAAAAATAAGGATGACATTTTTTTTCTAAAGCTGCTGTTTATTTCCATGATAAATCACCTTTCTTTTCTTGTATTCTGTAGTGAAAGTAAAATCATTCTTTTTTGGTAGACGCAGTGCCAGATAGATCATTTTTAGAGAATACATTTGGCCTTTTTGCGCTAACAAGTTGCACCTCTTTTGGGGAGGCGGGAATGAGCAGAAATATTAATTATGTCAGAAAAAAATTAGAAAAACAAGATTTGTCATTTTCAGGTGATTTGAAGGAGCCATAGATAAAAAGGTACTGACCTTTTCTTCACGGCTTTCCCACAGAGGCAGAATTGCCCGGGGGGCTAAAAGGAGCTGGCTCTAACATCTGGCTTTCAGTCCTGCTTCACCACTTACTGGCTGGGTGACTCCAGACCATGTGCCAGGGCAGCCCCTCTGAGACACAGACACTAAGATGGGATTAGATGGGCAAGAGGTTCATTGTGGGGAAGCCTGTGAGAGATGACCAGAAGGGGACAGAGATGGGGGCAGGCAGGGAGAGCCCGCAGATGGCTGTGGGCCTGCAGATACTGTGAGGGGAGGGCGCAGGGAGGACAGAGCCGGGTAGGAAGGGCCTCGGGTCGCAGTCCACAGACTGTAACACAGTCTCAGCCAGGTGCCTGCAGTGCCCCCAAGCAGAGATCATCTCTGAGAAGAGCTCAGTGTTGGCTATAAATGGCCCGGCTCTAATACCCCCGAGTGTCACTGAAGACCTAGGGCATGGCAGCCCCACTGTGCTCCCTGCAGCAGCTTCTCTTGGAGCACGACTTCATGGCTGCCACATGCCGTTTAACTTCTCTAAGCCTAAGCTGTCCCTCTATGCCTGTCTTGCGTGTTAGCAGATTGCTACCTCTCTCTGGACCTCAATTTTCCTGTTAGTTAAATGGGCTCGATGATGCTTTTCTTGCAGGGAGGAGAGGTCATAGCTTATAAGGAGGCTGGCCCTTGAAGCCCACTCAGCAAGCTGTGAGCATGCATCACAGGCAGAGAGAGGTAAAGGTCAGAGAGAGATTGACTGCCAAGCTCTGAAGGAGAAAGCCTGTGTGGACAGCTCCACGTCTCCAGCTGCCCCATGCAAAGTCTTGGGGTCCCTCATTTTCCAAAACTGTGCTAGTAGAAGCTAAGGCAGAAGGAGAGGAGATTGTCCCTCCAGTTGTCCCCTCCCCTGGCTACTCCTTGGTAGGGAGGCCCCACTCCCCACCCCTGCTCTCTTGGTCAAGCTGACCTTAATGACAATGACCTCCCTCTTTCTTTTCTTTTTTTTTTTTTTTGAGACGGAATATCACTCTGTCACCCAGGCTGGAGTACAGTGGTGCGACTTGGCTCACTGCAACTTCCACCTCCTGGGTTCACACTATTCTCCTGCCTCAGCCTCCTGAGTAGCTGGGACTATAGGCACCCGCCACCACGCCCGGCTAATTTTTTTGTATTTTTATTAGAGATGGGGTTTCACTATGTTGGTCAGGCTGGTCTCGAACTCCTGACCTCGTGATCCGCCCACCTCGGCCTCCCAAAGTGCTGGGATTACAGGCGTGAGCCACCGCGCCCGGCCAACCTCTCTCTTTCAAGAAACTGCCTGGAGGCCCCTTTCCCCAGCCTCCCGCCTCTGGCCTCCCCCTTGTGGCCTCTCCATCAGCTTGGCGCCCCCCCCCCGCCCGGCAGCTTCTCTCTCAACACATTCAGTGCAGTGAGTTACCAACTTCTAACGATTCAACCCCTGTGCCTTCCCGTCCAACATTAAACCGTACATCATTAATGAAAAAGTAACATTTTAAAAGGTAAAATTTTTTAAAAAGTCAAACAGTAAATATAATTTTCAACTTATATTTTAGCCCCAAATGTTGTAGCAATCAGTTATTTTCAGAAAGTTGTAAGAGTTGGAGGATTCTGTTGTTCTCATTCTGATTTACATTCTAGCAGTGTTCTGACACTCCTTTAAACTGGTGCCATTGCTTTACCCCTTTGGTGAATGTATAAAAATGCTCTTTAGCTCTCTGCCCTACCCTCCCATCCTCCAGCAATGAAGAGTCATAGCTACAGTATCATGTACTGGGATCTGAATCCACTGCTGCCTTTTTTTGGGTGTTAGTCAGTTAGTCTTTTATGAAAGAAAGTTGCTTTAGGAAACAGTTCTGGAAAGCAAATGTCAAATCTGATCACCAGGCCCACATATGGAAAGTACATTCTATTCTGCAGCACGTTCTAATATCCTCCTTAACTTGGCTACCCCTCATTCTCCAAACCTCCGCACTAACACACAGACACACCAAGAGAAATATTGAGCAGTGTTACCATCTGGTTGGCTTAATTTAACAAATATAGATTTCTCTTTCGTTTTGAAGAACATTGCCCTCAAGGAAACTTGCTAATCTGAAGAATAAATGTGCATCTTAGCCTCACAGAATTAAAAAGCAAAGAGAATTAACAGTATAATTTGTTTCTTCCACTTCTGGTTTCTGCCTCCAAATTTCCCATTTACCATTTAATTCAATTCAGTAACTATTTATCGAGTGCCTACTGCGTAATAGGCACTGGGGATGCCGCTGTGAGTGGGATGAACCCATGCCTCCTATCTGGTGTCTGCTTAAGACGTTAGCCACAGGAATGGCTGAGGACAGCCTGTTGACATCTGCATCTCCCACGACCCTTTCACGCACACCTTTATGCATCCCTCTCAGGGCACCCCTGCACCATAAACCACTCAAGGAAGGAAACATCCATCGTTGCATTCCTACTGTCCAGCACTGCACCTTATGCATCTTCCACACTCATTAAATACTTGTTTGATGGGTGGATGGATGGATGAGTGTGAGTTTTCATAAAAAGTAAAGCTTGCTTAGCTGGATGTGCATAGAACATGTAACCATCATGCAAATGAATACTAACTTGCACTCTGCTTTTTTTTTTTTTTTTTTAGACAGAGCCGCTGTGTCACCCAGGCTGGAGTGCAGTGGCACGATCTTGGCTCACTACAACCTCCACCTCCTGGGTTCAAGCGATTCTCCTGCCTCAGCCTCCCAAGTTAGTTGGGATTACAGGCACCACCACCACGCCCAGCTAATTTTTGTATTTTTAGTAGAGACAGGGTTTCCCCATGTTGGCCAGGCTGGTCTTGAACTCCTGACCTCAGGTGATCCACCCACCTCGGCCTCCCAAAGTGCTAGGATTTTCCCATAGTGCTGAGATTACAGGCGTGAGCCACCTTGCTTGGCACACTCTGCTTTTACTGTATGATATTTGCCTCATTCTTCTTCCTTCACAGGGAGGGTATTAGGGTCTAAGAAATGTAGAGATGGGTGGGAGAAGGTGGGTCTGTGCTTCCGTGTCTTTGGTTAAATCTGTCTAACAGAAAGGAAAGGCTTCTTTGATGCTTAAATCACATCCTTGTTATTCAAGTTGTCCCCTACTTCTCCTACGACTTCCCTCTCCACGAATACATACAAAACAGAATGCATATTCATTGAGTTTGAAAAGTACAGGCTTCTCAGTGAAATAAGCCAGTCACAAAAGGACAAGTCCCCTACAATTCCACTTACATGAGGTATCTCAAGTAGTCGTGTTCATCGAGAGAGAAAGTAGAGTGGTGGTTTGTTGTCAGGGGCTGTGGGAAGCGAGACTAGGGAGCTCTTGTTTCATGGGTACAAGTTTCAGTTTTGCAAGATGAAAAGAGTTCTCGAGATTGATTGTACAACAATCTGAATGTACTTAACAGTACTGAACTATACACTTAAAAAAGGTTAAGATGGCACATTTTAGGTTAGCGTATTTTACCCTAACTTTTTAAAACATGGACTTTTTATAAAAGATTCAGACATGTTTCTTCTTGCCATGTGCTGGGACTTACACCACTAGCTAAGTTTGCCACAAAAGTTCCATGTTATTCCCCAATGTAGTAAGGAAATTATACAACAAAACCATTAACAGCTGGAATAGAATAGCTTTTTAAAGTTTCCAGAGAAACGGGTCATTTAATCAGTACCTACGTTAGCTTATCCATTTGAAAAATGGGGGTTGGGTGTTTGCTCCCCACCCTCTGTCTCAGTGCTGAGATTCGAAGGAACGCTGAACACCTCTATTTCCCTTCATCGCCGATGTTCCCAACAG
Seq C2 exon
GTCACAGTTTGCTGTGGACATGCAGACAACATCCTCCAGAGGACTGGTGTTTCACACGGGCACTAAGAACTCCTTTATGGCTCTTTATCTTTCAAAAGGACGTCTGGTCTTTGCACTGGGGACAGATGGGAAAAAATTGAGGATCAAAAGCAAGGAGAAATGCAATGATGGGAAATGGCACACG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000053747-LAMA3:NM_000227:31
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.018 A=NA C2=0.016
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0221019=Laminin_G_2=PU(44.6=87.1)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
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:
No suggested primer sequences
R:
No suggested primer sequences
Band lengths:
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)