DreINT0057763 @ danRer10
Intron Retention
Gene
ENSDARG00000011956 | dlx4a
Description
distal-less homeobox 4a [Source:ZFIN;Acc:ZDB-GENE-980526-73]
Coordinates
chr3:34540568-34542351:+
Coord C1 exon
chr3:34540568-34541046
Coord A exon
chr3:34541047-34542157
Coord C2 exon
chr3:34542158-34542351
Length
1111 bp
Sequences
Splice sites
5' ss Seq
CAGGTAAAG
5' ss Score
9.65
3' ss Seq
TTTTTACTTTTTCACGCAAGATT
3' ss Score
3.88
Exon sequences
Seq C1 exon
CGACGCTGTTGAGATGAAGTTCTCAGACTTCACACACGGCCAAAACGAAAGCAAACGCACCAGCCCCACGGACATGGATCTCTTTGATGGCCCTCTTTAAGAGATGGAAATTACATGACTTCTAAATAGATGCCACTTTTATGGTGCACCGGTCTAATGGACATAACTCTAAAACATGACTATGACTTCATTGTCTGAAAGTTTGGAGGCTTCAGATCCCTCAAAGTCGGCTTTTCTGGAGTTCAGTCACGGTTACCAGTCTCACCAGCAGCATTCACCCGGTGTGTCTCACGCGCACTATCCGGTGCACGGTTTGCATCAAGGCGCGCATTCGCAATACGACGCGGCCTTCTCTCCTGGCGCTGCGTCTTACAGCCGTCCACTCGCTTACCACTATTCCACCGCACACCACCATCCAGGAGCTTACCTACCCTATCAACACAACAGCGCAGTCGGATATTCAAGAGTTGAGGATGCAG
Seq A exon
GTAAAGTGTGCTCTCATTCACTCACTAAAAATGGCATTGGAAAATTATGATACAAGGCGCTGGATTTCTGACAAATTTTACAATTGTGCAGTTTGGGCTCCATATTATTGTACTTTAAATATCTTTAATCACTTAGCTATTTGATTATTTTTTAAATCAAAAAGTAAAATTGATCCTGTGGAATTTATCGACGTTTTTTGTACGTTTACAAATTTGAAACAAACTGAGAGCCTTAAAAATATATGGAGAAATTAAGAAGTGTCTATATTTATTTAGACATAAAATAGACTTAAAATAATTATTTGTAAAAAAAAAAACAGTAGCTAAACTGACATATAAACGGGTGCATTTTTCATTGCTTTTTGCTTTAGTTTTTCCAACTAAATCCAGATAGTACTAAAATGCTACATTAAAATGTATGGCTACGCAGAAGGATTAATATACTGTGATCACTCCAATTAACAAAACAAGATTGACGGATCCCTAAAACAAACACATGCTTTATTTCAGGGTTTTATTTTATAATGGACATATAGCCTTGCTGCAATAATATACAAATCTCTTAAAAACAAATAAAAATTTAAAATGCCTTTTGGATGTTATAGAATTTTATATATTTATAATGTAAACCATATCTGAATACACACAGGTAGGTTACACGTTTCTCATTTGTTTAAACCCTGTCTTTAGGTATTAAAATCGCACAATAAAAAAGAAAAGAAAAATTAATTATAGTGATTGTTTAGTCGTCATATGGTTAACATTTAAAATGCATAATTTACAAATTATAGCAAATGTTTTCTTTATAATAATTTATCTGTCTTTTTCAATATAATGCAGTTTATCTAAAGCTGCAGATCATTCATTATATGCAACAACTTCAGTGATATTTTATACTCTACAACTGCAGTCAAAATGACAACGTGACAGTAGATTTCTTAGGGGTTTACAAACATTTTTATTGATTGACTGGTGAGCACATCTTTCAAAAAACAACCTAATAATAATAATAATAATAATAATAATAATAATAATAATAATTATTATTATTATTATTTTTATTAATGATATTATTATTATTAAATATGCTTTTTTTACTTTTTCACGCAAG
Seq C2 exon
ATTCCGAGAAGCAAAGTTCCATTGAAAGTGGAGAAATACGGCTGAACGGGAAGGGGAAGAAGATTCGCAAACCGCGCACGATTTACTCGAGCTTACAGCTGCAGGCGCTCAACCAGCGCTTCCAGCAAACCCAGTACCTCGCGCTGCCCGAACGCGCTGATCTGGCGGCTAAACTGGGTCTGACACAAACACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000011956:ENSDART00000133457:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.471 A=NA C2=0.338
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0004624=Homeobox=PU(73.7=64.6)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TCAGATCCCTCAAAGTCGGCT
R:
GCGGTTTGCGAATCTTCTTCC
Band lengths:
343-1454
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]