DreINT0167080 @ danRer10
Intron Retention
Gene
ENSDARG00000007863 | tra2a
Description
transformer 2 alpha homolog (Drosophila) [Source:ZFIN;Acc:ZDB-GENE-040426-1391]
Coordinates
chr19:20593564-20595119:+
Coord C1 exon
chr19:20593564-20593737
Coord A exon
chr19:20593738-20594985
Coord C2 exon
chr19:20594986-20595119
Length
1248 bp
Sequences
Splice sites
5' ss Seq
AGGGTAAGG
5' ss Score
9.16
3' ss Seq
ATGTATTGCTGTGATGTTAGGAA
3' ss Score
2.13
Exon sequences
Seq C1 exon
GATTCGCCTCCCACAGTACACCGCGCGTTTCAGATGGTCGGCCATTTTCTGCAGTTACATTAGGAGCGGAAGTCTTCGTCGAAGAGCGTCTTCATATCCACGCTTTTTTTTTTACCAGTCAATAATATTTTTAAAACAATGAGTGATACTGAAGAGCAACAATTCCAGAGGAGG
Seq A exon
GTAAGGATTTAATTTCGCAAACCTTTCTGCAGTTTTTTTTAGATATTCTTTCTTTCTCTTTACGGTAATGCTCGGTTTGTGAACAGCTAACGTTAACTTAGCTGTCCATTTCTTTTGTTTATTTACAACCTACCTAAACCGAAAGATTAGCTAATATATTATTGTTGGCCGATAGTAAGCAAAAGATTTACCATTTAGTCACTTTAAATCGTATAAGTCCTTTACAATGTTATTGTTGTGTAATGTTATTACGTTGCTATGTTGAATAGCATATATCGAGATATTTGTTTTTCACCATCATGTATTTATATAACGTTGTGTTGTTTTACTTGCTTGTCCTACAGCAATACACTCTGAAACAGAGATACAAGCACTTAAGTAATAACGTTACATCTCCCATTCACACAATAGCAGCCAGATTACTTTTGGTTTCTGTTTCCAGCATTTCTCATCTTTCCTCTTTCTCTCATACCATACCATAACCAAACAAACATCTTTATTTCACAAGGAGTAGTGAAATTTGAAGAGTTCAATTCATTTCCCCCCAAGTTTCCCTTGATCTTAATTGCTCTGAATGTTCTTTTTTCATTAAGGTTATTGGTCGTGAAGGATTTGAAGAGTTAAGGCCAAGAATGTGGAAGAATATTCAAGATAAAAGAAGGCTTTTACAGAGAAAATGTTTACAGAGCAGACGGTTAAGTGGGAAGGGGAAAAAAGAACGGAAGATCGGTCAGATAGAAGCACGCTTGCGTTATGTGTCTAAAGCAGAAAAAAGAAAAGAGGTTTCAGATTGGGGTGAAGAAATGAAAAGGAGAGGAAAAATGAAAACTGAACAAATGAAGACCGAAGAATAAAATGCCTGAAAGAAAGGAATAGCGTATACTGAAAACAGAAGAATGAATGAGTCCGTAGGCTAAGTAAATGCTAAATTTGTGTTCCAAGTGTTTCTAATCTCTTCTTAATTATCATTTGCATGTTTGTAGCTTTACTATGGTGATTCGGCTAATGAACAAGCATCACAAGGACACGTGATGACTTGCTAGCCTTTGTAAATGTATCAGTATTGCTGTTAACTTTTTTTTTTTTATTCCATAATATAATTTAAGTAATTCTAACACTTTCCTCCGCAGCTGTAGTAAAGTGAATGTTTGGATTACTGCTATTGTGAATGTGGTGTGAGTGTGTAAGTTAGCAAAGCTATGTTAATGTTTGTCTTGTACATGTCGTAATGTATTGCTGTGATGTTAG
Seq C2 exon
GAATCTCGCTCGGCGTCCAAATCGGATCGGGGGAGTCCTGCCCAACCCAAGATGGAGAGCAGGTCTGGTTCTCCCAGCCCTTCCAGAGCATCCAAGCGTTCTGATTCAAGATCAAGATCACGCTCCAAGTCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000007863:ENSDART00000008595:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.954 A=NA C2=1.000
Domain overlap (PFAM):
C1:
PF086487=DUF1777=PU(6.5=83.3)
A:
NA
C2:
PF086487=DUF1777=PU(21.8=96.4)
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GATTCGCCTCCCACAGTACAC
R:
TGGACTTGGAGCGTGATCTTG
Band lengths:
307-1555
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]