DreINT0025568 @ danRer10
Intron Retention
Gene
ENSDARG00000004880 | acsm3
Description
acyl-CoA synthetase medium-chain family member 3 [Source:ZFIN;Acc:ZDB-GENE-080220-22]
Coordinates
chr2:44872552-44875282:-
Coord C1 exon
chr2:44875163-44875282
Coord A exon
chr2:44874473-44875162
Coord C2 exon
chr2:44872552-44874472
Length
690 bp
Sequences
Splice sites
5' ss Seq
AAGGTAGAT
5' ss Score
7.24
3' ss Seq
TTTTGTTTACTTTTTTTCAGATT
3' ss Score
10.81
Exon sequences
Seq C1 exon
GTGGTGAAGGCTTTTGTTGTGCTGACAGCAGATTTTAAATCAAGAGCCCATAAGGAACTGATCAAGGAACTGCAAACACATGTAAAGAGCATCACGGCTCCTTACAAATATCCACGCAAG
Seq A exon
GTAGATTACCCACTTATTACTTTCAATTTGATTAGGTTGAAGGGATTCTGTTGGAGCCATTTGTTTACTTTATTTAAAGCAGAGATGCCCAAACTAGGGCCCACAGGCCAAAGTCAGCCCGTAGTAACCTTTGATTTGGCCCCCCATGCCATCTGAAAATGGTTTAGAGATTGTTCTTTCACATTTAATGTAATCTTCTATTTGTTTTTTTAAATTGTTAAGCTACAAATAAACCATCTAAAATTTAATGTTTCAATGTAAATTGTGTAAATTAATCAGATTTAGTTTAAATGTACATACGATGGTTTGAATCAAGGCAAAGGAAGATTCTGCTTGACTAGTGTATTCAGCATTGAACTCTACTATGTTATAAGTTTAATTGTTTTAATTGCAGTGGGTCGTAATTTAAAAAGTTATATTGCATTAGTTAATATCACTCAAAGTAAAGTTTTTTATTTATTTTTAAATATTATTAAGCGAACTTGGAAATTACCCATAGCAATTTTAATGTAAAATAGTTTGGTATATTTACCTTTGGCCCACAGCTATCAATGATATTTGGTTTTTGGCCCTTTATACGGACCAGCTTGAGCACCACTGATTTAAAGCTTTATATTGTTAATCATGATTTGTACGATCATGATCTTTCTGATTCTCTTTTGTTTCATCATTTTGTTTACTTTTTTTCAG
Seq C2 exon
ATTGAGTTTGTGGATCAGCTGCCCAAGACAGTAAGTGGGAAAATAAGACGAGTGGAGTTAAGAAAGAAGGAATGGGGACAGCAAACCAGCTAAATCTGGAACTGAGAAATCAAATGTAAAAATGGCATTCCACCTCTTCACATGCTACATTCACAAGTGTCTTCCCACATTTTTTAGAGATGCATGAAGAAGAGATTATTATGAAATGATTTTCAATATTTCAGCTCGCCAGCAGATGGCAGCACTTCATAATGTCTTCATTCAACATATGAACTCACCGGCCACTTTATTAGGTACTCCTTAGTAGGCTGGACCCTCTTTTGCCTTCAGAACTGCCTTAATCCTTTGTGGCATAGATTCAACAGGGTAATGGAAAATTCCTCATATTAGATTTTGACATGATAGCGTCACACAGTTGATGCAGATTGTTGGCTGCACATCCATGAAGCGTATCTCCCATTCCACCACATCCCAAAGATGCTCTATTGGATTGAGGGTCTGGTGACTGTGGAGGCAGTTTGAATACAGTGAACTCACGGTCATGTTCAAGAAACCTTCTGAGAGGATCCGCATTTATGACATGGTTCGTTATTCTGCTGGAAGTAGCCATCAGAAGATGGGTACACTGGTCATAAAGATATGGACATGGTCAGCATCAATACTCAGGTAGGCTGTGGTTTTAACACAATGCTCAGTGGGTACAAATGGGCCCAAAGCGTGCCAAGAAAATATCTCCAACACCATTACACCACCACCACCACCACCAGCCTGAACCGTTGATACAAGGCAGAATGGATCTATGCTTAATGCTGTTGATGCCAGATTCTGACCCCACCATCTGATTGTCACATAAGAAACCGAGACTCATCACACCAGACAACGTTTTTCCAATGTTCTATTGTCGAATTTTAGTGAGCCGGTGAGAATTGTAACCTTGTTTCCTTAGCATGCATTGAGTTCCTGCCATGTGATTGGCTGATTAGAATTTTTTTAACGAGCAGTTGGACAGGTGTACCTAATAAAGTGGCTGGTGAGTGTATTTTAACAGCTGTTAAATTTACTAACCCACATATAATTAATGTTTGTTTTTTTTACAATCTCTTTATTGTATTTTTTACATCAGTACTAATGATAACTTACATGTGTACTTTTTTTCGCTTTTAAACAGTTAACAACATGTTACTATTATATGCATAAGAGAACAAAAACAAAATTATAAAAGTGGAAGGAAGAGGCAAAAAAAAAAGAAAGGAGGAGAAAAAAAAAGTAAATAAGGGGGGATATTTGAGGCATTTCTACTAGGGTTCAATCACTGCTCACTGGTTAAAGTACTCAACAAATGTATTCCATATTACATGGAAATTCTTTGTTTTATTTTTTAGGGAAAGCCTTAGCTTCTCAAGTTGCAGACAGGACATGACATTTTTTTTATTAACGTGAAGCAACGTGGAGGATCTTTTCTATTCCAATTTTTTTAAACTAATCTTCATGCTAGGGTTATAAATCTGATTACTGTACATTAATTATATGATAATTCTGCATCATCACCGACTCCAAATTTAGCTAAAGTAGGCCCAGGGTATACTTTTTCCTCCACTTCTGATATGAATTTAAAAACTGAAATCCAATAATTAACAATTTTAGAGCAACTAAAATTAAACAACACTAAAAACTAAACAAGCGATGCCTGGGTTTGATTGCATCTATCACACAGTAGGTCTAAGGAAGGGAACATCTTAAAATTCATGTTTAAATAGAGTGACGTTATATTTAGACTTTTATATTGTACATCATATTCTGCACATGCAAATCAAAATGATTTCTTTGTTAAAAGAGTAAGCATTCATCACCATATTGTTTGGAGTTAATACGTTATTTTATGCGTGTGATTTTACAATATATAAACTTTGATTTATCAGTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000004880:ENSDART00000041806:12
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.033
Domain overlap (PFAM):
C1:
PF131931=AMP-binding_C=FE(48.1=100)
A:
NA
C2:
PF131931=AMP-binding_C=PD(16.0=41.9)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Mouse
(mm9)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AGCATCACGGCTCCTTACAAA
R:
GCAAAAGAGGGTCCAGCCTAC
Band lengths:
357-1047
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]