HsaINT0003014 @ hg19
Intron Retention
Gene
ENSG00000215009 | ACSM4
Description
acyl-CoA synthetase medium-chain family member 4 [Source:HGNC Symbol;Acc:32016]
Coordinates
chr12:7476869-7477194:+
Coord C1 exon
chr12:7476869-7476996
Coord A exon
chr12:7476997-7477094
Coord C2 exon
chr12:7477095-7477194
Length
98 bp
Sequences
Splice sites
5' ss Seq
TGGGTTTGT
5' ss Score
0.77
3' ss Seq
AAACTTCTTTTCCTCTTCAGGTA
3' ss Score
10.74
Exon sequences
Seq C1 exon
GACAATCCACAGAAAACTGCTGCCACGATAAGAGGAGATTTTTATGTCACTGGAGACAGAGGAGTGATGGACAGTGATGGGTATTTCTGGTTTGTCGGCAGAGCTGATGATGTCATTATATCCTCTGG
Seq A exon
GTTTGTATATTTGCCACTCTGAAGAGGTAACAATTCGACAGGGAGGGAGATCTCTAACTTGGAGGATGTGGTGGTCAAAAACTTCTTTTCCTCTTCAG
Seq C2 exon
GTACCGTATTGGGCCATTTGAAGTGGAGAGTGCACTCATTGAGCATCCAGCAGTTGTTGAATCGGCTGTTGTCAGTAGTCCAGATCAAATCCGCGGAGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000215009-ACSM4:NM_001080454:10
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:
PF0050123=AMP-binding=PD(9.9=95.3)
A:
NA
C2:
PF131931=AMP-binding_C=PU(32.1=76.5)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TGCTGCCACGATAAGAGGAGA
R:
ACAGCCGATTCAACAACTGCT
Band lengths:
180-278
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)