DreINT0065124 @ danRer10
Intron Retention
Gene
ENSDARG00000059255 | evx2
Description
even-skipped homeobox 2 [Source:ZFIN;Acc:ZDB-GENE-980526-215]
Coordinates
chr9:2001904-2003443:+
Coord C1 exon
chr9:2001904-2002668
Coord A exon
chr9:2002669-2003204
Coord C2 exon
chr9:2003205-2003443
Length
536 bp
Sequences
Splice sites
5' ss Seq
AAGGTAAAG
5' ss Score
9.06
3' ss Seq
TCTTTCGTTATCCGATTTAGGTT
3' ss Score
9.77
Exon sequences
Seq C1 exon
CCTGGATATACGCGTCTGGCCGATCAAGGGCCGACTCTATCAACCGATGACAGTCTCTCTCCTATTTATTTGCTTATAAACCTGTTACAATAAATGATCATTCGAGCCGCGTCACGCGCACCTTTAACGACGAAGGCGCAAACCACTTTTTGATGAATGACTTTCTGGACCAGAGAGGATGCGCGGGTCATTTTGAGCAGTCATTCGTTGCCCGCACTGGCATTCCTCTGTTTTTTTTTGCCTTCCAGCTCATAAAGGTGTTATATTATTTAGAGGCGGCAGCTGAGCTGAATGCGGATTAGATCCGCCACCAGTCATCGGAGCACCAGCCCTGGGACTTTGGATTTTTTCTGCACGACTTCATGATGGAGAGGATAAGAAAAGAAATGATTCTGATGGAAAGGGGACTACACAGTCCAGTGGCAGGGAAGAGGCTCTCCAACCTCACCGACTCGGCCGGGAACGCGGTGCTCGAGGCCCTGGAAAATTCCCAGCACGCAGGTCGCCTCAGCCCGAGAATAACTTCCGCCTCGCTGCATGGGGATATTCCCACCAAAGGCAAGTTCGAGATCGACAGCTTATTTGGGAACCACCACAACGACAACACTTCCTCAACAGAAGTGTCGTCCTCCGAAAGCCGGAAGAAAATAAACCTGTATCCTGAAGTTTCTCCTGACTCCGACATGAACAGCGATGTGGAAGTGGGCTGCCCGTCTCATCGTTCCCCGGGCAGCATCAGCCAACACAAGGAGAACAACAATAAAG
Seq A exon
GTAAAGAAATTGCGTGAAAAGGCGTTTTTTTTTCAATTTGTTTATGTCGATATTTATTTTTTAAAGATAACTGCTTTAGAATTTGGTTTATATTAATGGTTTAAATGTGCTTAGTATTTATTTTTTTTATTGTGTGTTCAGTAATATTTTAGTGTTGCATTTTTCCTAATGTCTGAGTGCTAGCATGTCGATGCATTTATCGAAATAAATTGTCTGTCGTTGCATTATGTAGTGTACACATTTAGCGTTTTAAAAAAAATATATATGCAAACGTTTGCATTTAATTGTGTATATGTAATTGCATTTTATTTTTTCCTTTAGATCTTTCGTTTATTCAAAATATTTTACACTGAATCTCTGAGTAAAAAAAATGTAATGCGATCCCAAAACGTTCCCGTTTAATTTAACTTATTTTACAAATGCATGATTTTCTTTGTTCATTATTTTAATGTTCAAATTAATGTGTTTTTTACCTCAAAATATATTTGTAAAATATTTATACATTTGAATTGTATCTCTTTCGTTATCCGATTTAG
Seq C2 exon
GTTTCTCGGACAGCAATTCAGGAGGCTCCAATACAAGTTCATCCTCTCTATCGAATCTTAACGGTAATTCCATGGGAAACAGCAGCTCGAGCTCGGACCAGGTGAGGAGGTACCGGACTGCTTTTACCCGAGAGCAGATTGGAAGACTGGAGAAAGAATTTTACAGGGAAAACTACGTCTCGAGACCCAGGAGATGTGAATTAGCCGCAGCATTAAACCTGCCCGAAACAACAATAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000059255:ENSDART00000082329:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.881 A=NA C2=0.575
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0004624=Homeobox=PU(77.2=55.0)
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:
CAACAGAAGTGTCGTCCTCCG
R:
CTCCTGGGTCTCGAGACGTAG
Band lengths:
346-882
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]