HsaINT0097325 @ hg19
Intron Retention
Gene
ENSG00000148356 | LRSAM1
Description
leucine rich repeat and sterile alpha motif containing 1 [Source:HGNC Symbol;Acc:25135]
Coordinates
chr9:130223452-130224652:+
Coord C1 exon
chr9:130223452-130223536
Coord A exon
chr9:130223537-130224530
Coord C2 exon
chr9:130224531-130224652
Length
994 bp
Sequences
Splice sites
5' ss Seq
AAGGTAGGG
5' ss Score
8.76
3' ss Seq
TGCTATTGGGGTCTCTGCAGACA
3' ss Score
6.98
Exon sequences
Seq C1 exon
GTCTTAAACGTGGAAAGGAATCAACTGATGCAGCTCCCACGTTCCATTGGGAACCTGACCCAGCTCCAGACTCTCAATGTTAAAG
Seq A exon
GTAGGGACCAAGAAGCCGTGTCCGTGTGACCCTCCATCAGCTCTGGGCCATCCTGGCCGGGATCCACAGGCTGCCCCGCCCGGGAGCCATTGAGCAGGAGGGCAGCCAGTCTCCGGGGGTCGCTGTAAATGGACTGACCCCTGCTGGGTCAGCTGTCTTCATGGTAACCAGAGACAGGCTGTCTGGAGGGTTCCTGTGGCTCCTGAGAGCCAGGGCCGTATGGCCGTATGGGGAGGAGGGCAGCTGGGCCCCGAGCCTCAGTCACTCATATTTATAATGGTGAGTGTAGAGGACTGATGGGGCGAGAGCTCCTAAGGAGCCGCAGTAAGGTTCTGAGCAGTGCTTCCACCTCCAGCGACGCACCAAGCCTCCTGAGGAGTCCACTGGGCAGGCTGAGGGCAGTGGTGCCATCCCCAGTTTACACACGAGGAAAACAAGGCCCGGGAAATCAAGTGTGACTTGCTCAAGACCACCCCGTGGGATGGTGACAGAGCCAAGACCACTGCACAGGCGCCTTACCCGCAGGAGCGCTCTGCTCGCCACACCCAGCTCTCTCCCTTCTCCTGGCTGTCCTTAAGCACTTCCTGCAGAGTGCCTCTGTTTATCAACTGTAACATATGAGTAATGAGAACAACAGTGGCGCCCCATTGCTCAGCCATTACAGCATGAGGGGCCCTGTGCGGAGGACCTCACACATCATCTACCTGAACCTCCAATCTCCCCGTGTTCTTATAAGGCTGGGTGGCAGTGTCATCCCCATTTTCCAGGTGAGAAAACTGGCACAAGGAGGCAAAGCCAGTTGTCTAAAGTCTCTTGGCTAGTAATTGGTGGAGTGGGGACTTGAACTGGAACTCCACCTTCTTGAGCCTAGGAAACCTCAGAGCCCAGGATCTGTTGTGTGCCCTAGAGGTCAGAGTGGCTCCCAGCGGGCATCAGGCAGGAAGCTGGTGATGGGGATTTGGGGTGTTGAGCTGTGCTATTGGGGTCTCTGCAG
Seq C2 exon
ACAACAAGCTGAAGGAGCTTCCAGACACCGTGGGGGAGCTTCGAAGCCTGCGTACCCTCAACATCAGTGGAAACGAGATCCAGAGATTGCCGCAGATGCTGGCTCACGTTCGAACCCTGGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000148356-LRSAM1:NM_001005373:8
Average complexity
IR-S
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:
PF127992=LRR_4=PD(40.4=65.5),PF127992=LRR_4=PU(20.0=31.0)
A:
NA
C2:
PF127992=LRR_4=PD(77.8=85.4)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GTCTTAAACGTGGAAAGGAATCA
R:
CTCCAGGGTTCGAACGTGAG
Band lengths:
207-1201
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Autistic and control brains
- 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)