HsaINT0003005 @ hg19
Intron Retention
Gene
ENSG00000005187 | ACSM3
Description
acyl-CoA synthetase medium-chain family member 3 [Source:HGNC Symbol;Acc:10522]
Coordinates
chr16:20803324-20803657:+
Coord C1 exon
chr16:20803324-20803451
Coord A exon
chr16:20803452-20803557
Coord C2 exon
chr16:20803558-20803657
Length
106 bp
Sequences
Splice sites
5' ss Seq
TGGGTAACT
5' ss Score
4.34
3' ss Seq
CCTGCCATATGTGTTTCTAGCTA
3' ss Score
7.03
Exon sequences
Seq C1 exon
GATAATCCTTCAAAAACAGCTTCAACTCTACGAGGCAATTTCTATATCACTGGGGACAGAGGATATATGGATAAAGATGGGTATTTCTGGTTTGTTGCAAGAGCAGATGATGTCATATTATCCTCTGG
Seq A exon
GTAACTTTCTTTTCCATATGTGCATATGTCTGTGTTAACTGATCATCAGTGTTCTAGAGTGAACCTGCCACTCACCTGTATGTATTCCTGCCATATGTGTTTCTAG
Seq C2 exon
CTATCGAATTGGACCATTTGAGGTAGAAAATGCCCTGAATGAACACCCTTCAGTTGCAGAGTCAGCTGTTGTCAGCAGCCCAGACCCCATCAGAGGAGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000005187-ACSM3:NM_005622:11
Average complexity
IR-C
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.147
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
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TAATCCTTCAAAAACAGCTTCAACT
R:
CTCTCCTCTGATGGGGTCTGG
Band lengths:
226-332
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)