HsaINT0090320 @ hg19
Intron Retention
Gene
ENSG00000130702 | LAMA5
Description
laminin, alpha 5 [Source:HGNC Symbol;Acc:6485]
Coordinates
chr20:60926965-60927416:-
Coord C1 exon
chr20:60927298-60927416
Coord A exon
chr20:60927136-60927297
Coord C2 exon
chr20:60926965-60927135
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-LAMA5:NM_005560:4
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
No protein impact description available
No structure available
Features
Disorder rate (Iupred):
C1=0.083 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0005512=Laminin_N=FE(15.4=100)
A:
NA
C2:
PF0005512=Laminin_N=FE(22.0=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
Associated events
Conservation
Rat
(rn6)
No conservation detected
Chicken
(galGal4)
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]
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)