HsaINT0003013 @ hg19
Intron Retention
Gene
ENSG00000215009 | ACSM4
Description
acyl-CoA synthetase medium-chain family member 4 [Source:HGNC Symbol;Acc:32016]
Coordinates
chr12:7456928-7459339:+
Coord C1 exon
chr12:7456928-7457128
Coord A exon
chr12:7457129-7459128
Coord C2 exon
chr12:7459129-7459339
Length
2000 bp
Sequences
Splice sites
5' ss Seq
AAGGTATAT
5' ss Score
7.84
3' ss Seq
TTCCATGTGTCCCTGGTCAGACA
3' ss Score
5.57
Exon sequences
Seq C1 exon
ATGAAGATTTTTTTCCGCTACCAGACATTTAGATTCATCTGGCTCACCAAGCCACCTGGCCGGCGCTTACACAAAGATCACCAGCTTTGGACGCCTCTGACTCTTGCTGACTTTGAAGCCATAAATCGCTGTAACAGGCCATTGCCTAAAAACTTTAACTTTGCTGCAGATGTGCTGGACCAGTGGTCCCAAAAGGAGAAG
Seq A exon
GTATATGACGATGGGCTTCCAGTAGATGCTTGGTGTCCCCTTATCTCTCAGTCTTCCATTTCCTTGTTCTGTGGTCTACCACTTAATTCCAATGCACTCTCTCACCCTCTTGGTTTCCTTTGTTTGTTTTCCAATTGCCCTCCCCTCTCCCCAGGGAAGATCTTAGATCCTCAGCCACAAATGGCTGGGCGGCTCTGGAGCCTTCTCTATCTCCCATCCCCATGGTCGTTCCTCACAGAGTTCTGCCTCTTTTCCTTCTCTTTTCTCCAAGCCCCATGCAACAGTGCTTTGTTTTCAAGTTGGTCACAGGCTTATCGAAAAAGTAGCAAATTGAGTTTTGATTTTATGAATACAGTTATCATTGGAGTAATGAGGAGAGAATTGGAGGTTGACAAGAATAAAGCAAGCGGCCCTTATGCAATGTTTACAGTGCAGCCTCAGGATGAGGTCTCTGTGTACTGATCCTCACCCCATGCCAGGCACTGAGCTAAACACTTAACCAAGCAGTGCTTATCAAAATGCACTGCAGGACCATGGATGGGAACATGATGTTAGGTACTAGACAGACAAGGTATTAAATAACATTGAATCAATTCTTCCTGTTAAATACAGGGGGAAAGCCTTCCTTGAAAGCCATTGTGTCTTTAGCACCTATCATTTGCTAAACACTCTCTTGAATAAAGACCACAGGTAGAAGCTAATCATCTCTAGATAAAATTTAATGGCATAGTTTTGTTTTCAGCATATTTATTTTTCAATAACCTATTTTTTGGCAAGTGGTAATAATTGTCCAATAATGGTGCTGATTAAATATATATTCCTTCTTAAGTAAATGTATACACGTAAAAAGTAAAAAGTGAGTCCATGTAGCGAAGTATACAAAATAAAGAAGAATAGTGCAGGTGCAGGCAGAGCTGACAGAAACAATGAGACTTAAATGACTAAAGATTGAGAAATACTGACCTATATTATTTCACCAAATCCCCATAACAACCTGGGAGGTTTGCAGATGAGGAACTTGACCTCATAGAAGCTAAGCTACTTATCCAAGGCCACACAGGTCCAACAGAACATAAACCCAGTCCCTGATCTTTACAGAGGTTACATCCACAGGGAAGAGACACATCTGTCATATAATAAATTGGAGTCATCTGGAGTATGAGCACAACGATGAAGGAACACAGAGAAGTTAGTGGAGAAACAAAGAGAAGTCTAAGAAAAGCTCACAGACGAACTGACATGTCAACAGGGCTTTAAAGTATTTGCCAGCCAGAGAAGATAAAAGAAGCATTCCAGATAGGGGAAAGAAGGGAGAGTAATTTTTTTCCAGGTAATACATAAGGCAAAGAGGTTTTGCAGTACAGATGACTCACTTTATAGAATGATGGGGAAGAAGTTACCTCTAGAAGTCAATAAATTGATGCCTCCCTCGACCCTGCTCCTTGTGACTTGTGAAAACCACACCTCAGCCTTAGGGTACAAAGAGATGTCTGCTTCCCAGTCAAACTTAGCAGATCCATTCAGGTTATTTGGATGGGAAAGAATCTAATTTAAGCAAGAAAGAAATTTATTCAAGGAATATGGGAGAGCTCACAAAATTGGGCTGGAAGCTGGAGAGTCCATCTCAATGAGGACAGGAATCAGGACAGCTCTCTGAGCATGCGTAAGCACGAATAACCCATAGACAAGTTTTGTACCAACCATTTTCTATCTTTTGATTTCTCTCAGAAAACCAAAAAGTCCAGAGAGAGAAGGTCTGATTGGCCCAACTTTGGTCAAATGCCCACCTACTGCTCGGGGAAGGGTAAAAGCAACCTGAGGGATTCTCTTTTCAAGGCTGTGTTCAATAGGAGAGGGGCAGTTCCCTCAAAGACGAACTCAGGGCGCTGTTAGCAGAATGCACCAGAACCAGTGCCAAAGGGGGAAAACAGCAGATGCCGCATGTAAGAGTAATCAGTCATGTAAACCTACCCCTCTCTTTTCCATGTGTCCCTGGTCAG
Seq C2 exon
ACAGGGGAGAGACCAGCTAACCCAGCCCTGTGGTGGGTGAATGGCAAAGGGGATGAGGTAAAATGGAGCTTCAGAGAACTGGGCTCCTTGTCCCGAAAAGCTGCCAACGTGCTCACCAAGCCCTGTGGCCTGCAGAGAGGAGACCGTTTGGCCGTGATTCTGCCCAGAATCCCTGAGTGGTGGCTGGTCAATGTAGCTTGCATACGAACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000215009-ACSM4:NM_001080454:1
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
No protein impact description available
No structure available
Features
Disorder rate (Iupred):
C1=0.030 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0050123=AMP-binding=PU(0.7=4.5)
A:
NA
C2:
PF0050123=AMP-binding=FE(16.9=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Rat
(rn6)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CCGGCGCTTACACAAAGATCA
R:
GCAAGCTACATTGACCAGCCA
Band lengths:
343-2343
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
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)