DreINT0110575 @ danRer10
Intron Retention
Gene
ENSDARG00000021336 | pax4
Description
paired box 4 [Source:ZFIN;Acc:ZDB-GENE-041210-244]
Coordinates
chr4:19714800-19715036:+
Coord C1 exon
chr4:19714800-19714882
Coord A exon
chr4:19714883-19714972
Coord C2 exon
chr4:19714973-19715036
Length
90 bp
Sequences
Splice sites
5' ss Seq
AAGGCAATT
5' ss Score
1.08
3' ss Seq
TTTTGATGTTTTGTTTGAAGGTT
3' ss Score
8.47
Exon sequences
Seq C1 exon
AGTTTACCTGTGGGCTTTATCCAGATCTGCTGACCAGAGAAAAGCTCGCAGAGGAGACAAACCTTTCACAGGACACTATCAAG
Seq A exon
GCAATTAAGATTTAAAAGTTAAAATGGTTGAACATTAGTCAAATGAAAAACAAATACATATCTGACTTGATTTTGATGTTTTGTTTGAAG
Seq C2 exon
GTTTGGTTCTCTAATCGTAGAGCGAGGATGAGGAGGGAGCGAAAGTTTGAACACAATGACTGTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000021336:ENSDART00000027919:5
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (disopred):
C1=0.964 A=NA C2=0.250
Domain overlap (PFAM):
C1:
PF0004624=Homeobox=FE(47.4=100)
A:
NA
C2:
PF0004624=Homeobox=PD(19.3=50.0)
Main Inclusion Isoform:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Rat
(rn6)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TTACCTGTGGGCTTTATCCAGA
R:
ACAGTCATTGTGTTCAAACTTTCGC
Band lengths:
143-233
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]