DreINT0025566 @ danRer10
Intron Retention
Gene
ENSDARG00000004880 | acsm3
Description
acyl-CoA synthetase medium-chain family member 3 [Source:ZFIN;Acc:ZDB-GENE-080220-22]
Coordinates
chr2:44876373-44878019:-
Coord C1 exon
chr2:44877892-44878019
Coord A exon
chr2:44876473-44877891
Coord C2 exon
chr2:44876373-44876472
Length
1419 bp
Sequences
Splice sites
5' ss Seq
AGGGTACAG
5' ss Score
3.14
3' ss Seq
GTGTGTGTGTGTGTTTTTAGGTA
3' ss Score
11.88
Exon sequences
Seq C1 exon
GGGGAGCCAGTGCGCACAGCAGAATGTTTCCGTGGCGATTTCTACCTGACAGGTGACCGGGGAATGATGGACGATGAAGGATATTTGTGGTTCATCGGCAGATCTGATGACGTCATCTTGTCTGCAGG
Seq A exon
GTACAGAATTCGGCTTTGATCATGATGATGTCAAATTTTAAATAAATATATATCATATAATAGTCTAACAAGTGTTTCTAGAAGTAAAAATTTTATTAATATGAAACTTTAGGGATTTTAAAGGCTAGACATTAAAAAAAAATCTGTGGTGAGCTCAGTTTTTTAACCGATAATATATTTTTTTAATAATCCTGTTTGTAAGAGTCTAAATTATCTTATGCATATGTTTATATGGTCTTTTTAATAAAAGAAGGCTCACACAAATTCCAAAAGGCAGATACTGATTAGATCAGGTCCTGGTGTGTGGACTTTGGGGGTTTTACAATGTGGTCACATGTTATTTAGTCAGTTTGAATGTCTCAGTATTTAAGCTTTGGTAACATTTGGTCAAGAAAGAGACAAATTAGGTGGTAAACTGCTCTGGCTTTTTCTCCATCTCTGCGCTTTCCTGCTCTGCTCCTCTGAGGTCTATCTTCTCTGACTCTACTGCAATCAGGCTAACTTCTGGGCCTCCTCTCTGTCTCTCTCCCTCCCTGTGTCTCATACCTCTGGTAACTTTATTTTTCTACATTTAAGCTGGGTGCAATTTATATCATATGTTTTATCATCATTTCATATTATCATTTTATAGTTATTTGTTATTAATTCCGTTGTAACCATAGAGAATTATTGTAAATTAAATCATCTCATTTTCATGTGAGAATTACTTTTGATTTAACATCAACATTTAATTGCTCCATATTGCAATACACTATAATCACACAATATCAACGCTCTCCCACATTTTAGGCTATTAACACTGCCCTTATTTCAGTTTTTGGTGTAAGATTGCAGAAGAATGGTTTGACTAGAAAGTACAGTTTTTTTTCTCTCCAATCAGAGTTACGGTGGGCAAATGCACCAAAAGATATCTTTAGAGCACTCCATATATAATTTGGTCTTCCTACACCAGAGGTACTCAACCTTGTTCCTGGAGATCTACTTTCTTGCAGATTTTAGTTGTAACCCATAACAAACACACCTGCCTGTAATTATCAAGTGCTGTTCATGCTCTAATTAATTGGCTCATGTGTGTTTGATCAGGGTTAGAGCTGAATTCTGTAGGAGGGTAGATCTCCAGAAACAGAGTTGAACACTCCTGCCCTACACTCATAAATGCTTAATTACTGGATATGTTTTGCAATTTTGTTCTGTCCCTTTAAATAATTCAATATAAATCATTAGGTAAACAGACTTTTGTTTTACCTTTTCTGTTATTTGTCCTATTCTCAAAAATTTCTTTCATACAAATTTAAGTTTGTTCTAAGTTCTTATAATGTTCCAACAAAGGCTTTTTAAATATCATAATGGGAAAAATTCAAGGAAAAAATATGCTTTTGAACATTTGTATAATATGTCTGTGTGTGTGTGTGTTTTTAG
Seq C2 exon
GTACCGTATTGGTCCATTTGAGGTGGAAAATGCCCTGATAGAGCATCCAGCTGTAGCTGAATCAGCCGTAGTCAGCAGCCCTGATCCTGTTCGAGGAGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000004880:ENSDART00000041806:10
Average complexity
IR
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
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GCACAGCAGAATGTTTCCGTG
R:
GAACAGGATCAGGGCTGCTGA
Band lengths:
207-1626
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]