HsaINT0097319 @ hg19
Intron Retention
Gene
ENSG00000148356 | LRSAM1
Description
leucine rich repeat and sterile alpha motif containing 1 [Source:HGNC Symbol;Acc:25135]
Coordinates
chr9:130263289-130265780:+
Coord C1 exon
chr9:130263289-130263422
Coord A exon
chr9:130263423-130265052
Coord C2 exon
chr9:130265053-130265780
Length
1630 bp
Sequences
Splice sites
5' ss Seq
GAGGTAAGT
5' ss Score
11.08
3' ss Seq
CTCCCGCTCTCCCTCCCCAGGCC
3' ss Score
13.15
Exon sequences
Seq C1 exon
AGCTGAAACCACCAATGGGTGAGGTCGTCACCCCTACGGCCCCCCAGGAGCCTCCTGAGTCTGTGAGGCCATCCGCTCCCCCTGCAGAGCTGGAGGTGCAGGCCTCAGAGTGTGTCGTGTGCCTGGAACGGGAG
Seq A exon
GTAAGTCCGGGGCCCTCCCCACCCGCCTGCCCTGCCTGTGGCCACCCTCCTCAAATTCTGCAGGTACAGGGTTGTCTCTGAACGTGTTTTCTCCAGTTCTCTAAGTAGACTGTGCTCATCTAGAAAGAAGGCAGGAAATAAAGATGACCCCTGGTCCCATGACCCAAATATGAGCTGCGCTCACATCATTTTCCGGACCTTTTTCTTTTTGTTCCTACTTAATAAATACATTAGGAAAAAATTTCCCAAATCATGAAATATCAACAACATGATTTACCCTGCAGAGGCTTTAGAAAATCATCTTTTGGCCAGGCATGGTGGCTCACGCCTGTAATCCCAGCACTTTTGGAGGCCAAGGCAGGTGGATCACCTGAGGTCAGGAGTTTGAGGCCAGCCTGGCCAACATGGTAAAACTCCATCTCTACTAAAAATACAAAAATCAGCCAGGCGTGGTGGTGGGCGCCTGTAAGCCCAGATACTTGGGAGGCTGAGGCAGGAGAATCGCTTGAACCCGGGAGGCAGAGATTGCAGTGAGCCAAGATCCCACCACTGCACTCCAGCCTGGCAGACAGATCGAGATTCCATCTCAAAAAAAAGAAAAAATCATCTTTTAAAAATTCATTAACACTTACTCTAAAAATTACACAGAGCAGTGAATGAAATACAAATCCTCCTTTGCCTCCACTGAGGGATCCTACTTAGAAAAGCAGCCATGTTTGCAGTTTGATGATTCCAGGGTCTCCCGTTGACCTGACTCATGCCATGATATGGATGGACCTATTGGTTCCAAATATAATCCCTGTTCTGGGGCCCTTGGCATTCCAGACAGCTTTGAGCGGAGCTTGGATCAGTTCCTGAAAGCAGGAGATGCTGAGGCAAAGTGTGGTCCTGAGTCAGTGGCTGCTGCTCCGGGTTGGGATTGTTTGTAGACTGAGGAGTTCAGGGCCTGGGCAAGTGCATCAACAAGAAAGAAGCCTGAACACCCTGCGTGCCCTCCGGCAGGGGCCGGCGGAATAGGCCTCCGTCGCCTGTCCAGAGCGCAGGAATATAATCCCCAGTTTTATTTAAGAAAGAATCAGTTGGGGCATTTATATGGGTATTTATATTTTTTACAAACTATAGAGAAATAGACAGCAAACTGCTAACAGAAGGCCTAGGTTACCTGTTTCGGCCGTGCCTGTTCTGTTTCTGTGGTGGTCAAATGCCCGAAGGCCCCACTATCAGGCGTTTATGGTAAAGATGCTAAAGAATAATGAAGGGGGCCGGCATGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGAGGCGGGCAGATCACTTGGGGTCAGGAGTTCGAGACTAGCCTGACCAACATGGTGAAACCCCATCTCTACTAAAAATACAAAAAATTTAGCCAGGTATGGTGGTGCACGCCTGTAGTCCCAGCTACTTGGGAGGCTGAGGCAGGAGAATCACTTAAACCCGGGAGGCTGAGGTTGCAGTGAGCTGAGATCCCACCACTGCACTCCAGCCTGGGCAACAGAGTGAGACTCTGTCTCAAAAAAAAAAAAAAAAAAAAAAAAGACGGGCCTGGGACTCCTGGAACCCGGTAGGGCCAGCCACATGCTCCCGCTCTCCCTCCCCAG
Seq C2 exon
GCCCAGATGATCTTCCTCAACTGTGGCCACGTCTGCTGCTGCCAGCAGTGCTGCCAGCCACTGCGCACCTGCCCGCTGTGCCGCCAGGACATCGCCCAGCGCCTCCGCATCTACCACAGCAGCTGAGTGCTGCCCGCCCACCTGGGCCTGGTCCTAGCCCTGCCTCGGCCACTGTGAGCCCCGGGCTCCTGCTCAGCCTTGTGCCAGCCAGACTCGTATGAGGCTCCCCCCTGCCCTGGGCCCCTTCCCCACTGCCCAGGAGCCCCCATCCTAAGCTCCAAGCATGTCTGGGCCAGGCAGAGGTGCTCCTCATCCATGACACCACCAGTCTGAATGGTCCTGGGGGCTGGGGCTGGAGAGGCCGCTGCACCACCACCCGAGCCTGGGAGCCAGCGTCCCAGCCTAATCACGGATCTGCTGCCTCCCAGCTGTCTTGACTGAAGGCCACCGCCCCTGCAGGAGCTTGGGTCCTCATCTGGGGGCCATGCACAGGCCCGTCCCACCCTGCATGTGGGAAGGGAGCAGGAGGGCCTGGCTGGGTGAGGGGAGGCCTTCCTGGGAAGGCGTGTGGTGCAGGCCTGTGCTCACAGTGGCACCAGCAACCCTGGGTCTCCCTCTCTGCTGCTCCCCAGAACCCCGGGGCCCTCCTGCTCTCCACAACTGTCCCTCCTTACCCCATGTAGCTCGATCCGAAGCAGGAGTGTCAATAAACCTGTCTTCAGTGCGCT
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000148356-LRSAM1:NM_001005373:25
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.556 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF139201=zf-C3HC4_3=PU(23.9=24.4)
A:
NA
C2:
PF139201=zf-C3HC4_3=PD(71.7=78.6)
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:
CTCAGAGTGTGTCGTGTGCC
R:
TGGTGGTGTCATGGATGAGGA
Band lengths:
358-1988
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Genotype-Tissue Expression Project (GTEx)
- 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)