DreINT0025576 @ danRer10
Intron Retention
Gene
ENSDARG00000004880 | acsm3
Description
acyl-CoA synthetase medium-chain family member 3 [Source:ZFIN;Acc:ZDB-GENE-080220-22]
Coordinates
chr2:44877892-44880031:-
Coord C1 exon
chr2:44879930-44880031
Coord A exon
chr2:44878020-44879929
Coord C2 exon
chr2:44877892-44878019
Length
1910 bp
Sequences
Splice sites
5' ss Seq
ACGGTACAT
5' ss Score
6.53
3' ss Seq
AATCTAAATTCATCCTAAAGGGG
3' ss Score
3.06
Exon sequences
Seq C1 exon
GTGGTGGATGAAAATGGCTCTGTTGTGCCAAAAGGACAAGAGGGAGACCTCGGCATCCGAGTGAAACCAGAGAGACCCTTCTCTCTTTTTACAGAGTATACG
Seq A exon
GTACATTTAATGCTTCTTCACTATCTGTATCTGTCTTCTTTACTATATTACTACTGAAAGATTCTACATTTCTTAAAATATATAAATTGTTTTACACCGCAAGATGGTTCTGACAGTATCACTTATTCAAATTAATGCAAATTACAAGTTCTAGGCACATCAGGTCTGACTTCCTATGTGTGAAATACAGCATCATGTCTCCATTGTAATGCGTATTGTCAATTTCAGTGTCTTATGTCTAACAATTGGCCGGGTGATACTTTCAGGCAAGGCCCAGAAAACAAGACTAAACTGTAATGGCAGTTTCTGTTTCAACTAATAAGCACTGCCCACTCAATTGTGTATTAAACTGCGAGCCAGCTGCAGTAGTCGAAAACATTTTCGATGAACGCCACAGCCAGTCCTTATTAAAGGATTCTGCTTTCAAGATATACAAAAATCTTCCTGGTTTTGTCTCTTCTTCAAATTCACAACACAAAACTAATAATCGACAACTGTTAAGGAATCCCACCTTCAATAAGCGTGTTGGTTTGGAAAGCTGTTTTCAAAGCATATTGCCATATCCACTTAAGATGTAAATTAAGTCCATGTGAAATCATAATTTATAAGGTTTATTCTGCTAGAGCACTTGGTTATACTTTAGGTGAATAAGTGCAGTTAATCTACTGGGGAGAAATGTAATGTAATGTAATGTATTCATATAGCGCATTTATTGTGTATGGTCACACACCCAAAGCGCTTTACAATCATGAGGGGGTCTCTCCACACCACCACCAGTGTGCAGCATCCACTTGGATGATGTGACGGCTGCCACAGGACAACGGCGCCAGTGCGCTCCCCACACACCAGCTATTGGTGGAGTGGAGAGACAGTGATTGAGCCAATTCGGTGGAAGGGGATGATTGGGAGGCCATGATCGTAAGGGCCGGTAGAGGGACTTTGGCCAGGACACCGGGGTTACACCCCTGCTCTTTCACGAGAAGTGCCATGGGATTTTTAATGACCACAGAGAGTCAGGACCTCGGTTTAACGTCTCATCCGAAAGACGGCGCCCACTGACAGTGTAGTGTCCTCTTCACTCTTACTGGGGCATTTGGACTCACACAGACCACAGGTTGAGCACCCCCTGCTGTCCTCACTAACACCACTTCCAACAGCAACCTAGTGTTCCCTAGTGGTCTCCTATCAAGGTACTGACCAGGCTCAGCCCTGCTTAGCTTCAGTGAGTAACCGGTCTTGGGCTGCAGGGTGACATGGCAGAAAAAAAAAATTTGTTTTGGTAATCTTCAATCAAAGTCTGAGCATTTATCCTTTCTGTGCCACGATATTCTTAACCACGCCACTCTTAAATGTTAGGTGCTATAAAGTAATGACGTTCAAAAAGAAAGCCCCGTCCCCTACACAATATTCCATTTCAGTTAAAAGTACATCAACGTTAACCGCAACATCCGGTTAACGTTGATTTGAATCAATCAGGTTTGTCAAGGTAATATAGTAGACAGGTGCAGGATGCTATATTTTGGTTTGTGGATTATTTCCACAATAAAGAGCTTGGATTTAAGATCACTTTGAGCTTGTTTATATTTGCATCTCTTAAGGGGGTCGCACACCGGTTGCGTCGTGCACATGACAGTTGGAAGTATCGCACACCAGTTGTGCACATTCGAATGGCATTTAATATGAAACCCTTCAGATGGCGCGGCAGAAATATAAACAGTATCCAGAGTCGTAGCTGGGCGCCGTGGACAGCCGCCAACTTGCAGCACCATTGTGCGTACACTGATCGAAATCTGTGTTTAGAATTCTAAAATGCAGGCATCCGGTGTGCAACAACCTTTAGTTTAGTTTTGTAAAGAAATGCAAAGTTAACAACTAAATTATTTGAATGTGAATCTAAATTCATCCTAAAG
Seq C2 exon
GGGGAGCCAGTGCGCACAGCAGAATGTTTCCGTGGCGATTTCTACCTGACAGGTGACCGGGGAATGATGGACGATGAAGGATATTTGTGGTTCATCGGCAGATCTGATGACGTCATCTTGTCTGCAGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000004880:ENSDART00000041806:9
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.088 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
Conservation
Chicken
(galGal4)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GTGGTGGATGAAAATGGCTCTG
R:
CCTGCAGACAAGATGACGTCA
Band lengths:
230-2140
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]