HsaINT1017962 @ hg38
Intron Retention
Gene
ENSG00000053747 | LAMA3
Description
laminin subunit alpha 3 [Source:HGNC Symbol;Acc:HGNC:6483]
Coordinates
chr18:23898954-23899455:+
Coord C1 exon
chr18:23898954-23899065
Coord A exon
chr18:23899066-23899287
Coord C2 exon
chr18:23899288-23899455
Length
222 bp
Sequences
Splice sites
5' ss Seq
ACAGTAAGA
5' ss Score
5.96
3' ss Seq
GACCACTTGATGTTTCCTAGTTC
3' ss Score
4.75
Exon sequences
Seq C1 exon
GCTCAAGTAAATTCCAGAAAAGCACAAACATTAAACAACAATGTTAATCGGGCAACACAAAGCGCAAAAGAACTGGATGTGAAGATTAAAAATGTCATCCGGAATGTGCACA
Seq A exon
GTAAGAAGAGTTATTAAGCCCAATTACATTTTTTTTGGTTACATAACCTTCATTGTACACTAAAAGAATTCCCTTTAAGATTTCAACATTATGAAAAGAATCCCATAGTGATACTAAAAAACTAATATAAAATCTCCATAGAAGTTTCTACCTTTTTTTTTTTTTAAGTAGCCTACTGGAGCCCAGAATTCCCAGTCTAATAGACCACTTGATGTTTCCTAG
Seq C2 exon
TTCTTTTAAAGCAGATCTCTGGGACAGATGGAGAGGGAAACAACGTGCCTTCAGGTGACTTTTCCAGAGAGTGGGCTGAAGCCCAGCGCATGATGAGGGAACTGCGGAACAGGAACTTTGGAAAGCACCTCAGAGAAGCAGAAGCTGATAAAAGGGAGTCGCAGCTCT
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000053747:ENST00000313654:46
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.581 A=NA C2=0.614
Domain overlap (PFAM):
C1:
PF060089=Laminin_I=FE(33.6=100),PF060089=Laminin_I=PU(1.0=2.6)
A:
NA
C2:
PF060089=Laminin_I=FE(21.0=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GCTCAAGTAAATTCCAGAAAAGCACA
R:
AGCTGCGACTCCCTTTTATCA
Band lengths:
278-500
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Autistic and control brains