HsaINT0003024 @ hg19
Intron Retention
Gene
ENSG00000215009 | ACSM4
Description
acyl-CoA synthetase medium-chain family member 4 [Source:HGNC Symbol;Acc:32016]
Coordinates
chr12:7476055-7476996:+
Coord C1 exon
chr12:7476055-7476156
Coord A exon
chr12:7476157-7476868
Coord C2 exon
chr12:7476869-7476996
Length
712 bp
Sequences
Splice sites
5' ss Seq
GTGGTATGA
5' ss Score
5.27
3' ss Seq
ATGTCATCCTTGGTTCCCAGGAC
3' ss Score
8.32
Exon sequences
Seq C1 exon
ATTATAGATGAAAATGGCAATGTTCTACCACCTGGCAAAGAAGGGGAAATTGCCCTCAGACTCAAACCTACACGGCCCTTCTGTTTCTTCTCTAAATATGTG
Seq A exon
GTATGAGGATAGAAAGTGCTGGTCATGCTTAATACAGACTTGGGTTCAAATTTCATTTCCACCGTGTCTTGCTATGTAATCTTGGGCAAGCAACAAAATCTTTCACAACTGTAAAATGGGGAGACTATCATCTGTCACCCAAGAGTACTGTAAAGATGAAATTCCAAATGTAAGAAACCAGTTGCAGTGGTTATCCTCAGAAAGGAAAACCGGACAGGCTGGAATGAGGGTGCAGTTGGGGGGTGCTAGAGGTAGAAGAGGGGCTTTTTATTATACTCTTTATGACCTTTTGTATTTTATATTACAAACTATCTTTTAAAAAAATTTAATTTCCAGCCAGGCACAGTGGCTCACGGCTATAATTTCAGCACTTTAGGAGGCCGAGGTGGGAGGGTGGCTTGAGCCCAAGAGTTCAAGACCAGCCTGGGCAACATAGTGAGAACCCATCTCTACAAAAACATAATACGGTTAGTCAGGTGTTGTGGCACATGTCTGTGGTCCCAGCTACTCAGGAGGCTGAGGTGAGAGGATCACTAGAGCCCAGGAGGTCGAGGCTGCAGGCTCCAGTCTAGGCAACAGAGAGAGACTCTGTCTCAAAAAAAAAAAAATTTCCTATATAAGTAGGATGTGTAATGTACTAGTCACTTAATGAGTGCCATACCCATCTCTGTTCTGACCAGACTAATCCCCAAATGTCATCCTTGGTTCCCAG
Seq C2 exon
GACAATCCACAGAAAACTGCTGCCACGATAAGAGGAGATTTTTATGTCACTGGAGACAGAGGAGTGATGGACAGTGATGGGTATTTCTGGTTTGTCGGCAGAGCTGATGATGTCATTATATCCTCTGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000215009-ACSM4:NM_001080454:9
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=FE(8.0=100)
A:
NA
C2:
PF0050123=AMP-binding=PD(9.9=95.3)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Rat
(rn6)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TGAAAATGGCAATGTTCTACCACC
R:
CCAGAGGATATAATGACATCATCAGC
Band lengths:
222-934
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)