Special

DreINT0025570 @ danRer10

Intron Retention

Gene
Description
acyl-CoA synthetase medium-chain family member 3 [Source:ZFIN;Acc:ZDB-GENE-080220-22]
Coordinates
chr2:44886073-44887721:-
Coord C1 exon
chr2:44887514-44887721
Coord A exon
chr2:44886217-44887513
Coord C2 exon
chr2:44886073-44886216
Length
1297 bp
Sequences
Splice sites
5' ss Seq
GGGGTGAGT
5' ss Score
7.93
3' ss Seq
ATGTTATGTTTGTGTTGCAGAAG
3' ss Score
9.75
Exon sequences
Seq C1 exon
GTACAGTTCTCATTCCTGGCACCTCTCAGCTCACAGCTCGAGATATGCGTCACAGACTGATAACGTCTGGGGCCAAGTGTGTGATCACAGATGAAACTCTGGCTCCACTGTTGGACACTGTAGCCTTAGACTGCCCTTCCATTTCCACCAAGCTGCTGCTGTCCCACAAGCCCATGGACGGCTGGGGCAACCTGACAGAGCTCATGGG
Seq A exon
GTGAGTGGAGAACAAGGGAGGGAATGGCATGTACAGGGGGCACTTAAAAAATTATAATAATAAAAAAATATTTAAAGTGACTGTTCACCTAAATAGATAATTAAAGGAATACAAAGGATACATAAAGGAAATTGACTAATTTTACAGCTCCCCTACATTTACAGATATTTCAGTTTTACCATTTTTTAATTCATTCAGCCAATCTCTGGGGGGGGTCTTGTGGGAGCAATTTTATCTTAGCTTAGCATAAATAATTGAATTGGAATAGCCCATTAGCATATCCATCAAAAAAATAAAATAAAATGATAATTTTCCCATTTAAAGCTTCACTCTTCTGTAGGTACATTGTGTATCAAGGCAGATAAAAAGTTGCTATTTTGTAGGGCCATATGGTTTGGAACTAACCTATCTTTCTGGCATAATAATTAAGGAACTTTGCTGGTGCACCATGGCTGCAGCAGGCACAATGATACTACGCAGCACCAGAAAATAGTCCAACGAGATAAGTAGGTAGCAACGCTGCATAAGATCATTGCACCTGCTGCAGCTATAGTCTTAGTACACAATGTACCTGCAGCAGAGTCAAACCTTAAATAGGAAAATTATCACAACTTTTTATTTGAATGAAATGCTAAAGGTCTAATCTGATTCAATGATTTATGCTAAGCTAAAAGTGCAAAAAAAGGTTAAAAAAATAAAAATAAACTCTAGGGGAGTTGTAAAATTTGCATTTTTGAAAAAAAAAGCAGTGTCCCTTTACACCAAGTTGTTTCTCAAGAGATTCTCTGCTGAACCCAAATTAAGAGATATTTACAGATCTAAATGTAATATAAATGTAAATATCTCAATTTGTGTTCAGCAGAGAATTCTTGAGAAACAACCTGAGGTGTAAAGGGACACTTTTTTTGCAAATATGCAAATTTTACAACTCCCCTAGAGTTGAGTTTATTTTTTCTTTTACCCTTTTTTGCACTTTTAGCTTTACTTAGCATAAATCTTTGAATCAGATTAGATCATTAGTATTTTTCTCCAAAAAAATAAAAATAAAATAAAGTTGTGATAATTTAAGGTTTGACTTTGCTACAGGTACATTGTGTACTAAGACCATAGCTGCAGCAGGTAACCAAGAGTTGCTGGTCTCCAAAACTTCTATACTATTGCCACCAACTTTCTTAAAATCTGTGTTTTAGAAATAAAGATTTTGAACAACTTTTCAGCAAGTAAACAATAACAGAATTATTTTTTAATATATATAAAGCTTTAGTGAGTAAATTAAGATGTTATGTTTGTGTTGCAG
Seq C2 exon
AAGAGTATCAGATGACCATGTTTGTGTGGACACCAGCAGTGAGGAGCCCATGACCATCTTCTTCACCAGTGGCACAACGGGCTCCCCAAAAATGACCCAACACAGCCACTGTAGTTACGGTTTGGGGCTCACCGTGAACGGCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000004880:ENSDART00000041806:3
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=FE(16.6=100)
A:
NA
C2:
PF0050123=AMP-binding=FE(11.6=100)


Main Inclusion Isoform:
NA


Main Skipping Isoform:


Other Inclusion Isoforms:
NA


Other Skipping Isoforms:
NA
Associated events
Conservation
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
ACAGTTCTCATTCCTGGCACC
R:
GTTCACGGTGAGCCCCAAAC
Band lengths:
345-1642
Functional annotations
There are 0 annotated functions for this event


GENOMIC CONTEXT[edit]

INCLUSION PATTERN[edit]