DreINT0057757 @ danRer10
Intron Retention
Gene
ENSDARG00000079964 | dlx2a
Description
distal-less homeobox 2a [Source:ZFIN;Acc:ZDB-GENE-980526-212]
Coordinates
chr9:3427979-3429216:-
Coord C1 exon
chr9:3428717-3429216
Coord A exon
chr9:3428164-3428716
Coord C2 exon
chr9:3427979-3428163
Length
553 bp
Sequences
Splice sites
5' ss Seq
CTGGTAATG
5' ss Score
5.67
3' ss Seq
TTGTTTGTTGTCTCTCCCAGAAA
3' ss Score
10.31
Exon sequences
Seq C1 exon
CCTCCCGCATCTCTGCTGACAGACAATCACAGTTCTGCTTTGCGTCGCGGTTGTTTTCTTCCAAAGTGGAATAGTGCAACAGAACTCAGAAAGCCTACTTAGTTTTGCGCCTTTGAAGATTTTTTTTATGGCTTCACTCTGTCGTTGGACTTGCTTTTAAGTGTGCTTTTGCGGTATGAAAAACATGACTGGAGTTTTTGACAGCCTCAGTACAGATATGCATTCGAACCAGATTACCTCCAGCAGTTACCACAGTCTGCACAAGTCCCAGGAATCGCCGACTCTTCCGGTCTCCACCGCTACCGACAGCAGCTACTACAATAATAATAACCAGCAGTGCGCTGGCTCTCCGTACGGCCAGATCAGCTCTTACCAGTACCAGAACAACAGCATGAACAGCGTCCAGTACAACACTAAATCATACGAGCTGGGCTTCGGAAACGCTTTCGGCCCCTACGGCACCTACGGCTCCTGCTCCTCACCAACTCCTGCAGATGCTG
Seq A exon
GTAATGATCTATGTGGTTGATATTAACCAATATGAGTAATTATCGCTGTAATTAATTTAAAATCGCAAAGTTACTGTGTATTAACACAACTTATTAAGGTAAAGTTGGTTTTATATTTGCACATTCGTTCGGGGATGCCACCTATACTGTTTACTATGGTACTTCGGTCTTAACACGTAATTATGACTTCAAAACAACATTAGCACAATTTATTTGACTGTAATCATGATTGTACTTTTATAGTCATTGGTTCCTAATATGATTTAAAATTTGCAAACAATAATATTCTGAAATTATAGGCTCTTATTAATAAACTCCGATTGTGTGAATAGAAAACCAACTTTACCGCAAAACACAACTTGTAGTGTTTATTACAAAACATAAATCATTGCGTTTTTATATGCACTTTTCTATAGTATACTCTATTATGTGTGTATAATATAGGAAATCTAAATATTGTTTATTGCATCACATAGAGGTTTCATTATACATATATAAAATGTTTCCATTAGAGTTCAATTCATTTACCACATTTGTTTGTTGTCTCTCCCAG
Seq C2 exon
AAAAGGAAGAAAGCGAACCTGAAATCCGAATGGTCAATGGAAAGCCAAAGAAAGTCCGAAAACCTCGTACTATTTACTCGAGTTTCCAGCTGGCGGCCCTGCAGAGGAGGTTTCAGAAGACTCAGTATCTGGCCTTGCCGGAGAGAGCTGAGCTGGCCGCATCTCTGGGCCTCACGCAAACACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000079964:ENSDART00000111386:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.486 A=NA C2=0.306
Domain overlap (PFAM):
C1:
PF124133=DLL_N=WD(100=69.7)
A:
NA
C2:
PF0004624=Homeobox=PU(73.7=67.7)
Main Inclusion Isoform:
NA
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:
CACAGTCTGCACAAGTCCCAG
R:
GCCAGCTGGAAACTCGAGTAA
Band lengths:
344-897
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]