DreINT0057755 @ danRer10
Intron Retention
Gene
ENSDARG00000013125 | dlx1a
Description
distal-less homeobox 1a [Source:ZFIN;Acc:ZDB-GENE-990415-48]
Coordinates
chr9:3416570-3417465:+
Coord C1 exon
chr9:3416570-3417016
Coord A exon
chr9:3417017-3417265
Coord C2 exon
chr9:3417266-3417465
Length
249 bp
Sequences
Splice sites
5' ss Seq
CAGGTAAGA
5' ss Score
10.77
3' ss Seq
CTTTTCTTTCTCCCTCCCAGCAC
3' ss Score
10.13
Exon sequences
Seq C1 exon
CAGAGACAAACTACATTTTCTTATGAATGGAAAGTGAAAAAATCAGTTGAGCTTAAATTGGGATCCATCCTTCACTCAGATCATAGAAGAAAACAAAAAAGCAGGGAGAGAGAGAGAGAGCGAGAGCGAGAGACATGACCATGTCTACAATACCAGAGAGTCTAAACAGCCCAGTCTCAGGAAAGAGCGTGTTCATGGAATTTGGGCCACCAAGTCAGCAAATGTCGCCTTCATCTATGACCCACGGACATTACTCAATGCACTGTTTACACTCCTCCGGACACCCGCAACACGACAGCGCATACAGCCCGGCTCCGTCCTTCCCTAGATCTCTGCCTTATCCATACGTCAACTCGGTCGGTAGCCATTCCTCCAGCCCGTACCTCAGCACCGTGCAGACCTACCCAAACAACTCGGCTTTGGCGCAGACCCGATTGGAGGACCCAG
Seq A exon
GTAAGAAATGCTTTGGTCTTTTTGCTGGTCGCTGCTTTTGTCGACGCACTACGAGAATGTTGGACTGGAGTAGCCCAGATGTGCTGTTATTAGGCTTGGTAATTATTTATTGCGTAATGCTATAAACAATGTATGCAATTAAGGCTAATTATACCTAAAGTGCCGCCTGTAAAACTTGTGCACAGTGATGTGAGCCGCACTGCATGAGCAGTCTGTGAGACAGTTTCTCCTTTTCTTTCTCCCTCCCAG
Seq C2 exon
CACCGGAGTCAGAGAAAAACACCGTGGTGGAAGGAGGAGAGGTTCGTTTCAACGGGAAAGGCAAAAAGATCCGCAAGCCCCGGACCATATACTCCAGTCTCCAGCTGCAGGCTCTGAACAGGCGGTTCCAGCAAACCCAGTATCTGGCTCTGCCAGAGAGAGCCGAGCTCGCCGCATCACTGGGGCTCACGCAAACACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000013125:ENSDART00000019910:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.771 A=NA C2=0.358
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0004624=Homeobox=PU(73.7=62.7)
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:
GCGTGTTCATGGAATTTGGGC
R:
AACCTCTCCTCCTTCCACCAC
Band lengths:
305-554
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]