DreINT0034743 @ danRer10
Intron Retention
Gene
ENSDARG00000004270 | atl3
Description
atlastin 3 [Source:ZFIN;Acc:ZDB-GENE-041010-109]
Coordinates
chr14:30446065-30448122:+
Coord C1 exon
chr14:30446065-30446136
Coord A exon
chr14:30446137-30447930
Coord C2 exon
chr14:30447931-30448122
Length
1794 bp
Sequences
Splice sites
5' ss Seq
AAGGTTTGT
5' ss Score
7.81
3' ss Seq
GAATTCCCCCTAACTGTTAGGTG
3' ss Score
4.23
Exon sequences
Seq C1 exon
GCTACAGCAGAGGCCAATAACCTTGCAGCTGTGGCCTCCGCTAAAGACCAGTACTACAAGAATATGGAGAAG
Seq A exon
GTTTGTATGTTTTCTGGAGTGTGGTTAGCAGCACTCAGTTGATGTATGATAAGTACAGTTTTTATCTAAAATGCATACAGATGCTGAATGTTTTTTTTTTTTTATGTGACAAGTCTCATTAAACTGCAAGTTGCAATTTAAATGTAAAACAGGCTTCTGGTAGCTCCAAATATAATGAAACGCAGAAATTGTTAGCATTAAAGTTTTACAACTAATCCTTTAACATGGTGTTAGTGTTGTCTTAAAGTATTAAAAGTTGATAAATCAATGTAGAGAAATTTAAGGCCCTTAAAGTATTTAAAAGTCTTTTTTTAGGACCTTAAAAAGCATTAAATGCTATTTTGCAAGGTATTAAATTGTATATAAGTATTGATTATGCAATGTACAGTTCAATACTTAAGTTTGCCTGAATGAAATCTGCACATATCAGGATGCTGAGTAGTTTATGAAATCAATGATATCCTGCTAGATTTGACATCCTGCTGCTTTGTTTACTGTAGTAACCAAGTTAACACCATTATTTTTGCAGTTCTATTGGCGCCAACCTGCTGAATTAGCTAGATTTAATAGATTTCTCTTCAGTATATGAATAATGTTTTAGTTTTGAAATAGTTTCTTATATTGATATTTAGTAAATATACTGCACGTTAAAATCTCACCAGTGTTTTCAGGTGAAAAATGGTTATAAGGTTCTAAAATTTATGGAAAGAGTCTTTAAAAAGATCTTAAAAAGTATTGAATTTCACTCTCTGATTCTTGTATATACTCTGTTTAAAGCATGGATTTACTGAGGAAACTCCTGGAGGGCTACAGCTCTGCACAGTTTAGTTCCAACACACTAAAGCCTCAGTCACACTGCACTTTTCGCCCCATAGACTTCTTCCATTCATATTTATGCGAATGCGACAGACCTAAAACGCAAGCTTGTGCGACAAGTTTCGCAGTTTGCTACTAAATTCAAGCTTGGTGAACTGAGCTGGGAAATTGCATCACAAGGCTACATAAGAGCAATCGAAGGTCAAAACATGACCTATCTGGACAGGAATTAAAAATTTCTCATGCACAAACTCTAATGTGACCACGTCATAAAGCACAATTCTGTTGTACAGCACTGTTAAAAGGGGCGGGATTGAACGAGATGATTAGACATTAAAAAAAAAGCGAGCCATTGGTCAATGTTTTAAATCTGTCCAGAGAGGTCATGTTTTGATCTTCGATTGGTCTCATGTAACCATGTGATGTGATTTCGCAGGTCAGAGTTCACCAAGCTTGATATTTTCAACGCAGCGAACTGCAAAACTTATCACATAAGCTTGCGTTTCCTGTCTGACGCATTTGCATGCATATGAATAAAAGTCTATAGGAAATCTAAAAGTGCAGTGTGACCACAGCTTCACCTTTTAATTAGGGTCAGAAGAGAACTGTGGAGAGCCGTGGCCCTCCAGTTTGACACCTGTGCTTTACAGTGTTCAAAATAGAAAAAGGAGTAGAAGGCCAGTATACGTGATGTTAATTATAATTACATATTACTCAAGTTGCTTTGGAATATAGTTTGCATATGTACATTATATTCGTGGAAGTATAATATATTCCCACAAATTCCCACAAATTCAAAATGCCAGGATTGATAAATTGGAGGCTGTTAAAATGTTGCAGTTCATAATATCACTTGTATAATTCTCACAAATTTGCATTGTTCAAACTACTGACATTTGCATTGGCATGTTGTTTCCAAACACAATATTCCAGACATAATTGAGTATTTATTTTTCATGAATTCCCCCTAACTGTTAG
Seq C2 exon
GTGTGTGGTGGAGATCTGCCTTACGTGGCCCCCAACTCACTGGAGGAGAAGCACCGATTCTTCCTGCAGGAAGCCCTTCACCTCTTCTCCAGCACTAAAAAGATGGGTGGACAGCATTTCTGCCACCGCTATCAGGAACAGTTGGAAAAAGAGCTGAAAGAGATGTGGGAAAACTTAAGCAAGCACAATGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000004270:ENSDART00000023054:11
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:
PF028419=GBP_C=FE(18.1=100)
A:
NA
C2:
PF028419=GBP_C=FE(49.6=100)
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:
GCTACAGCAGAGGCCAATAACC
R:
CATTGTGCTTGCTTAAGTTTTCCCA
Band lengths:
262-2056
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]