DreINT0104766 @ danRer10
Intron Retention
Gene
ENSDARG00000039095 | nkx2.3
Description
NK2 homeobox 3 [Source:ZFIN;Acc:ZDB-GENE-990415-178]
Coordinates
chr13:40285486-40286018:-
Coord C1 exon
chr13:40285938-40286018
Coord A exon
chr13:40285832-40285937
Coord C2 exon
chr13:40285486-40285831
Length
106 bp
Sequences
Splice sites
5' ss Seq
TAGGTATGT
5' ss Score
7.76
3' ss Seq
TTGTAGATGTAATCCAACAGCGC
3' ss Score
2.75
Exon sequences
Seq C1 exon
CGCCGATGAGTGGCGGTCCTCACCTCTCTTCATGCAAATCAAGCAGCCATGACAAAATGGGAGATTAATCGACACATTTAG
Seq A exon
GTATGTTTACTTGAAATTGTTGCTTATCTAAACAATTGTTCAACAAGGCTTAGTGCTCGAAGCTGCCATTTGAAGCAGGGATAACATTGTAGATGTAATCCAACAG
Seq C2 exon
CGCCTGATGATGCTTCCGAGCCCGGTCACATCAACGCCGTTTTCTGTGAAGGATATACTGAAACTGGAGCAGCAAACTCGCCAGCTTCAATCTCTGCACCCCGCGTCGCACCACGCGCAACTGCATCCGGAACTGCAGGATAGATTTCAGGCACCATCGTCGTGTTTTCTCGGAGGTGGAGACAGTCCCGGCTTCTCAGACAACGAGGAGAAGATGTCTTTTCTGAACTCTCTCTCCATGCAGGACAGTTTAGTGGAGAGCAGCCTTTCCCCGCCGATGTTCGTCCACCCGGCCCTGGGACACGTCGACACTAAACTTGAAGATGAACTTGAGGACCACGAAACGA
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000039095:ENSDART00000057094:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
5' UTR
No structure available
Features
Disorder rate (Iupred):
C1=NA A=NA C2=0.586
Domain overlap (PFAM):
C1:
NA
A:
NA
C2:
NO
Main Skipping Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Human
(hg38)
No conservation detected
Human
(hg19)
No conservation detected
Mouse
(mm10)
No conservation detected
Mouse
(mm9)
No conservation detected
Rat
(rn6)
No conservation detected
Cow
(bosTau6)
No conservation detected
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GCGGTCCTCACCTCTCTTCAT
R:
CTCCACCTCCGAGAAAACACG
Band lengths:
250-356
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]