HsaINT1017996 @ hg38
Intron Retention
Gene
ENSG00000130702 | LAMA5
Description
laminin subunit alpha 5 [Source:HGNC Symbol;Acc:HGNC:6485]
Coordinates
chr20:62351909-62352360:-
Coord C1 exon
chr20:62352242-62352360
Coord A exon
chr20:62352080-62352241
Coord C2 exon
chr20:62351909-62352079
Length
162 bp
Sequences
Splice sites
5' ss Seq
GAGGTGGGC
5' ss Score
6.32
3' ss Seq
TCACCGCATACTGCCCACAGATC
3' ss Score
8.29
Exon sequences
Seq C1 exon
CCTCCAAGAGGGACTGTCTGGAGCGGTTCGGGCCACAGACGCTGGAGCGCATCACACGGGACGACGCGGCCATCTGCACCACCGAGTACTCACGCATCGTGCCCCTGGAGAACGGAGAG
Seq A exon
GTGGGCCGGGGAGGGGCAGGGCGGTACGGGGGCTGGAGAACGGAGAGGTGGGTAGGGGAGGGGCAGTGCCGAGCGGGGCTGGAGAAGGGAAAGGTGGGCCCGGGAGGGGCAGTGCTGAGCAGGGGCTAGGGCCACACTGGCGTCACCGCATACTGCCCACAG
Seq C2 exon
ATCGTGGTGTCCCTGGTGAACGGACGTCCGGGCGCCATGAATTTCTCCTACTCGCCGCTGCTACGTGAGTTCACCAAGGCCACCAACGTCCGCCTGCGCTTCCTGCGTACCAACACGCTGCTGGGCCATCTCATGGGGAAGGCGCTGCGGGACCCCACGGTCACCCGCCGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000130702:ENST00000252999:4
Average complexity
IR
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(15.4=100)
A:
NA
C2:
PF0005512=Laminin_N=PU(66.7=96.3)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TCCAAGAGGGACTGTCTGGAG
R:
CATGAGATGGCCCAGCAGC
Band lengths:
252-414
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Autistic and control brains