HsaINT0002968 @ hg19
Intron Retention
Gene
ENSG00000166743 | ACSM1
Description
acyl-CoA synthetase medium-chain family member 1 [Source:HGNC Symbol;Acc:18049]
Coordinates
chr16:20636745-20638638:-
Coord C1 exon
chr16:20638511-20638638
Coord A exon
chr16:20636845-20638510
Coord C2 exon
chr16:20636745-20636844
Length
1666 bp
Sequences
Splice sites
5' ss Seq
TGGGTAGGT
5' ss Score
6.86
3' ss Seq
CAGAACCCTTCATCCTCCAGGTA
3' ss Score
8.78
Exon sequences
Seq C1 exon
GGTGACCCAGAGAAGACAGCTAAAGTGGAATGTGGGGACTTCTACAACACTGGGGACAGAGGTAAGATGGATGAAGAGGGCTACATTTGTTTCCTGGGGAGGAGTGATGACATCATTAATGCCTCTGG
Seq A exon
GTAGGTGTGGCTGATGCTGGGCTGGCTGTTGTTGCCGTCACATGCCTCACGGAATTTTGCTTACCTAGACATTTTTTCACGCATTGGTGAAATTTCAGCCTAAATCTGAATAGAGCCGTGTCTATGGTGCCCTGATTCCAGGCTTCAGTATACCTCCCGAACCTTCTCTGCACGCAGAAGAATCAAGCAAAATGAAATTCAAGAGGGTCTGGAAGAGGAGCCATAATAAGACACTGTGCAATTTACAGTGGGGTGGGGGGAGTGGAATTGAGAAGGGAGACTCTGTCTTGGTCTCCATAGGTTCAGGGAGCCTATTTCATGTTTGTGCCCCTCTAATGCAGCACCAAATGTCACAGGACAAACATAGTAATAATAATAGCTAACCTTTAGCTATTGTTTATTTTTATTATTATGAATATATTTGTTATACATCTATGAGCATAATAAATCTATTATTATAAAATTATTTATTAGTATAAATATATTATTTACTGTAACTATTTAGCTAACCTGGAGTACTTACTATGTGAAAACACTGTCCTTAATGCTTTATATAACCCACCTCTCAAAGCTGGATGGGAGATGTGATTATTATCCCTATTTTACTAACGAGGAAAGTGGGTCACTGACCGGCAAGGAAATTTGCCTAAAGATTCAAAGATAGCACAGGATGCAATCCAGATTTGAACTGAGGTAGTCTGGCTCTGAGTCCCTGTCCCTACCCCTACATGATTTTTAAAAAGGCGCATTACACTACAGTAACAATTTCCCTTGGATATTTTAGAGAAATTGATGGCATTTTTATTTTTTTATTTTATTTTTTATTTTATTTTATTTTATTTTATTTTTCTGAGACAGAGTCTCCCACTGTCACCCAGGCTGGAGTGCAGTGGCCTGATCTTGGTTCACTGCAAGCTCTGCTTCCTGGCTTCAAGTGAGCATGTCCAGCTAATTTTTATACTTTTAGTAGAGATGGGGTTTCACCATCTTGGCCAGCCTGGTCTTGAACTCCTGACCTCCATTGATCCCCCTGTTTCAGCCTCCCACAGTGCTAAAATTACAGGTGTGAGCCACCATGCCCAGCCTGGATGGGATTTTATTTTAAATTTCTAAAACATGATGTACTGGAAATTTGCACAAAGAGTAGATTTTATGTTCTTACCACAAAAGAAAAAAAAGGCAATTATGTGAGACGATGGATATGCTAGTGTGCTTGAGTGTTTTAATCGCGTTACTATGTATATGTACATCAAAACATCATGTTGTAAGCCTTAAGTATATATAATAAAAGCCGAAAATCCTGCTGATACAATGGGAAATAGTATGCAGAATTTGCATGAATGTTTAAGACCAAGTTTGAGGCTTCCAAGAGATTTCGTGTTGGGGGAAGCTGCTTGGGCCAAGCTCTGAGGAGACAAAACATTAGCCGTCCTCCATCAGTACAGGCAGTGAGGCAAGAAGCCGGGAGCACCGCAGTCTTGTATTTCTCAGCCTATAATGTCCAGGTCTTTACACTTTGGGCCCATGACACAGACAAGTCAGGGGTCCCTGGCTTCCTATGACCTCCACCCTCTGTGCCAAAGGAAGCTGTGACTCCAAAGCAGGAGATCTGGGGACTTGGTTCACCCCAGCCCTGGCATCTGCCTCAGAACCCTTCATCCTCCAG
Seq C2 exon
GTATCGCATCGGGCCTGCAGAGGTTGAAAGCGCTTTGGTGGAGCACCCAGCGGTGGCGGAGTCAGCCGTGGTGGGCAGCCCAGACCCGATTCGAGGGGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000166743-ACSM1:NM_052956:10
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.087 A=NA C2=0.081
Domain overlap (PFAM):
C1:
PF0050123=AMP-binding=PD(0.1=0.0),PF0050123=AMP-binding=PD(91.3=95.5)
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:
GGTGACCCAGAGAAGACAGCT
R:
CTCCCCTCGAATCGGGTCTG
Band lengths:
228-1894
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)