DreINT0110574 @ danRer10
Intron Retention
Gene
ENSDARG00000021336 | pax4
Description
paired box 4 [Source:ZFIN;Acc:ZDB-GENE-041210-244]
Coordinates
chr4:19714600-19714882:+
Coord C1 exon
chr4:19714600-19714713
Coord A exon
chr4:19714714-19714799
Coord C2 exon
chr4:19714800-19714882
Length
86 bp
Sequences
Splice sites
5' ss Seq
AAGGTGATT
5' ss Score
5.88
3' ss Seq
TCTGATTTCTGATCAATCAGAGT
3' ss Score
4.41
Exon sequences
Seq C1 exon
AACAACTGAATGTACAGAGCCATTTTCAGCAACAAATGAACACAAACTTGCCAAGAACTGCTCATCGAAGCAGAACCGCATTCACAGCAGATCAGAGCGGGAGATTAGAGAAAG
Seq A exon
GTGATTCAGCCACTTCAATCTCTCATAGTCAGTTCTGTGTTGACAAAAAGACATTATAACATCTCTTCTGATTTCTGATCAATCAG
Seq C2 exon
AGTTTACCTGTGGGCTTTATCCAGATCTGCTGACCAGAGAAAAGCTCGCAGAGGAGACAAACCTTTCACAGGACACTATCAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000021336:ENSDART00000027919:4
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (disopred):
C1=1.000 A=NA C2=0.964
Domain overlap (PFAM):
C1:
PF0004624=Homeobox=PU(29.8=43.6)
A:
NA
C2:
PF0004624=Homeobox=FE(47.4=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Rat
(rn6)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
ACAGAGCCATTTTCAGCAACA
R:
TGAAAGGTTTGTCTCCTCTGCG
Band lengths:
169-255
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]