HsaINT0097316 @ hg19
Intron Retention
Gene
ENSG00000148356 | LRSAM1
Description
leucine rich repeat and sterile alpha motif containing 1 [Source:HGNC Symbol;Acc:25135]
Coordinates
chr9:130257599-130258374:+
Coord C1 exon
chr9:130257599-130257697
Coord A exon
chr9:130257698-130258242
Coord C2 exon
chr9:130258243-130258374
Length
545 bp
Sequences
Splice sites
5' ss Seq
CAAGTAAGG
5' ss Score
7.66
3' ss Seq
TACACGTTTCTGTCTTGCAGGAA
3' ss Score
11.38
Exon sequences
Seq C1 exon
ACGGAGTTAGAAGCCAAAAGTGAAACCAGGCAGGAAAATTACTGGCTGATTCAGTATCAACGGCTTTTGAACCAGAAGCCCTTGTCCTTGAAGCTGCAA
Seq A exon
GTAAGGACTGCTGGTGCCTGTCCCGGCCAGGGAGCCCTGGGGACCTCCTCCCAGAGGCGCCTGTGGTGCCTCCACCATGCTCTGCCTCTTGTTACTTTTCTGGTGACTCTAGCATGCCAGATCCTGTGCCAAGCCCCAGTGGAGACAGAAGCGAGAGTAAGGGAGTGTTCATTCTGGTGAGGGGGACGACAAGGCACTGGTCACTGCTGTGCAGGGCAGAGACCACTGAGCCCACAGTAGAGCAAAGCCTGTGCCGGGAGCCACTGTCTGTCCAGCACCTGCGGGGACAGAGAGGCAGTTGAAACAGCCCCCTCTTGGTGGATGTTCAAGTTGCTTACTATTTTCAGGTTTGCAGACAGAGCGGCAGTGAACCCCTGGGCCTATCTATCTATCTATCTCTGTGTGCCTACCTATGAGTTTTTGTAGGAAAAATCCCGAGTACATTCTATGTATTATGTTATAAATATTCAAACCCTTCATTTCCTGTTGTAAACAGTGGGTTCTTTTCTTCCTTCCTGCTCATGGTACACGTTTCTGTCTTGCAG
Seq C2 exon
GAAGAGGGGATGGAGCGCCAGCTGGTGGCCCTCCTGGAGGAGCTGTCGGCTGAGCACTACCTGCCCATCTTTGCGCACCACCGCCTCTCACTGGACCTGCTGAGCCAAATGAGCCCAGGGGACCTGGCCAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000148356-LRSAM1:NM_001005373:22
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.038 A=NA C2=0.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0764712=SAM_2=PU(64.4=86.4)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
ACGGAGTTAGAAGCCAAAAGTGA
R:
AGGTCCCCTGGGCTCATTTG
Band lengths:
224-769
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)