DreINT0057758 @ danRer10
Intron Retention
Gene
ENSDARG00000079964 | dlx2a
Description
distal-less homeobox 2a [Source:ZFIN;Acc:ZDB-GENE-980526-212]
Coordinates
chr9:3425857-3428163:-
Coord C1 exon
chr9:3427979-3428163
Coord A exon
chr9:3426913-3427978
Coord C2 exon
chr9:3425857-3426912
Length
1066 bp
Sequences
Splice sites
5' ss Seq
CAGGTACAA
5' ss Score
7.09
3' ss Seq
TAATTTCTATATATCTTTAGGTT
3' ss Score
8.42
Exon sequences
Seq C1 exon
AAAAGGAAGAAAGCGAACCTGAAATCCGAATGGTCAATGGAAAGCCAAAGAAAGTCCGAAAACCTCGTACTATTTACTCGAGTTTCCAGCTGGCGGCCCTGCAGAGGAGGTTTCAGAAGACTCAGTATCTGGCCTTGCCGGAGAGAGCTGAGCTGGCCGCATCTCTGGGCCTCACGCAAACACAG
Seq A exon
GTACAAAAGCTTGATATACATCAAATATCGGCCATCATATAGTTTAATTATGAATTTATTTCTAAAGTGTTAATTGGTAATAATAATATCAACCTGTGATTATATTATATTAAGAACTATTAAACCATTAATCCTAAAGCCTACTTCTTATTCATACTGGTTTTAGTTGTAACATTATTATAAACACTGTGCGTTGGTATGGCTACATTTTGTTTAAATCCACCCTATTAAATATTGCACTGTAAAATAAATTAGCAATTAGTTCTGACAGTTTGTTTAGGTCATTGTAAACTAAGTCAATCATGTTCTAACTTAATTTGAAAGGTTTTGCGAGCTGTTTTAAATCAGTTTATCATAATATACGTTTAATGGATTCATAATTTGATTCAGCTTAAAAAATTAAGGCAACCAGGATTATTTACAGTGTGGTTACACTTAACAATAAGATTGAATTAGTTAATGCATTTACTAACATGAACAAACAATGAACAATGCATTTATTAGCATTTGTTCATGCTAGTTAACGTTAGTTAATGAAAATAGGTTATATGTGTTAGTTGCAGCCGTTAGTTCGTATTAATAAATTAGTAGTTCGTGTTACTAAATAACTAATGAAACATTATTGTAAAGTGTCAGCAATATTTATACACACACTCAAATGCTGGGTTGTCATTTCCCAAAGTTGCTCAAATATGGACAAAGTTAGTGGTTGGGTTAAAAGCGTCATTTAATTATTATTTGATAGGAAAATTAATGAATTAATGACAACCCAGCGTTTTTAAGTGTTTAAATATTTTAACTTAAGGTCGGGGTTTATGTATAACAAATTGTTAGCCAGCCCACATAGTCAATCTTTTTGTAAATGTTTTGTAAAACATGCTTATATAGCCTAATTTTTATTTAGGCCTATATATATATATATATATGCTATGAATATTTTAACGCATGGGGTTGATTTGTTGCATATAGCAAATTGTGAACTAGCCCACAAGGTCATTATTTTGGTGAATGTTATTTGCTTACATGTTGCTCTAGAGCAATTTTATTAATTTCTATATATCTTTAG
Seq C2 exon
GTTAAAATCTGGTTCCAGAATCGTCGTTCAAAGTTCAAGAAGTTGTGGAAAAGTGGAGAGATCCCACCCGAGCAGCATGTGGCCTCCAGTGAGTCTCCACCTCACCCCTCACCGCCTCTCGCCGCGGCCTGGGACTTCGCGCACAGCCAGAGAATGAACACTGTAAACTCGGGTTTGTCGCAGAGCAGCCCTCCCAACACAACCACCCCTTCCTTTCTGACAAACTACCCCTGGTATTCATCCACGAACTCTGCGGCCCACCTTCAGCCACCACTTCATCACAATACAACTGTTAGCGCCGGGACCATATTTTGACTCTGCCGACTTGGGGAACTCAGTTTGTGAACTGAACTTAAATGACTTTTAGGCCTGTTTGGCAGTCTTGAGTGGTGAGACCTCGATCTGCACCGATGCCACGTTGATCATTGCCAGTGCGATTTGGGCGTGACACTGTTACTTTTCATGCAATGTCGCGTCAGCAAGCAGACACTACAGAATCAAACATATACAATTATTTTTGTATTTATTTATTTTGTTCTATGAGTGGTACGTCTATGGATTAAAGTGAACTACAATTATCCAAAGCCTAGAGAACTCATGTGGACATTATTGGAGTAAATATTTGCAGCAGGGTGAATCAGAGCACATGTAGCACAACCTGAAGCTGTTTGGTGCCTTCTTGAAAATAACCTGACTTGTCGGTTTCCATGTGTTTCATGCGCCTGTCTTTACTTTCAGATTTGTTTTTGTTCATTTTATATTTAGTAGCCTATACGCAAGGTAAGTTGGAAATTTGGTGTCCGTCTTTGTATATGTCCCATCGCGTCTATTTAATAATGTTGTTATTCGTATAGGATATCATAAGAGTTTCACTGTTTAAACACTAATGAAAATCACACGCAAGCTACTGATTGTCCTAAAGTCATGTATATATTTTTTTTCCTGGAGTTCTTTGTTTTATTTATTTTGAAGCCGAATGAACATCTCTGCCACTATAATGATTCAGACTTATTTAAATAAAATGTTTCATGTGAATGCACTGTTTGTGTGTAAATT
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000079964:ENSDART00000111386:2
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.306 A=NA C2=0.510
Domain overlap (PFAM):
C1:
PF0004624=Homeobox=PU(73.7=67.7)
A:
NA
C2:
PF0004624=Homeobox=PD(22.8=12.4)
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:
CCCTGCAGAGGAGGTTTCAGA
R:
CCGCAGAGTTCGTGGATGAAT
Band lengths:
345-1411
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]