DreINT0104767 @ danRer10
Intron Retention
Gene
ENSDARG00000039095 | nkx2.3
Description
NK2 homeobox 3 [Source:ZFIN;Acc:ZDB-GENE-990415-178]
Coordinates
chr13:40283325-40285831:-
Coord C1 exon
chr13:40285486-40285831
Coord A exon
chr13:40284333-40285485
Coord C2 exon
chr13:40283325-40284332
Length
1153 bp
Sequences
Splice sites
5' ss Seq
CGAGTGGGT
5' ss Score
2.58
3' ss Seq
CTGTATCTCCTGTCTGACAGAGA
3' ss Score
7.9
Exon sequences
Seq C1 exon
CGCCTGATGATGCTTCCGAGCCCGGTCACATCAACGCCGTTTTCTGTGAAGGATATACTGAAACTGGAGCAGCAAACTCGCCAGCTTCAATCTCTGCACCCCGCGTCGCACCACGCGCAACTGCATCCGGAACTGCAGGATAGATTTCAGGCACCATCGTCGTGTTTTCTCGGAGGTGGAGACAGTCCCGGCTTCTCAGACAACGAGGAGAAGATGTCTTTTCTGAACTCTCTCTCCATGCAGGACAGTTTAGTGGAGAGCAGCCTTTCCCCGCCGATGTTCGTCCACCCGGCCCTGGGACACGTCGACACTAAACTTGAAGATGAACTTGAGGACCACGAAACGA
Seq A exon
GTGGGTGATTTAAGTTTTACCGCTGACTAAAATGAGGTTGAAGCAGGCGATGAGGTCGAATTGCATATCTCTGTATAAAAGTCAGGGCCAGAAAGAAACGAGAAAGTACTAAAACGAGAAAAGAAAGACGAGGATTAAGTGTATTTTGATGCGTAAAATGTAACATCTAAATAATGAACAAATAATGAAAACCAACAACAACAAAAAGCATCGTCGATTTAACTTAAACATTAATTTATAACAACTAAAGTTTTGAATTAGGTAAAATTGCTCTTTATTTTTAAAAACAGTACATATGTACATAATATATAATTGTTGTTTTTATACCATGTAGCTTAAATATAGATCACAAATACATAGTTAACTTAACTGAGGCTATCAGCACTGGCTAGCATTAAAATGCATACATTTTAGGTCTACCAAAGATTTGTTTCTTTCCCAGGGATGTTAAAATTTATCTTTAATTTTGAAAATATATATTATTTTTGATTAGTGACCTATTATTGATTGTAGATAACTGTAAAAAGAACTTAAAACTTGATGTGTAGGCCTGCTATATGTGTATTTTGAACTCGTCTTCAAATATAGCCTAGTTAAATAATTCTTCAAGTATGTAATTAAGTTTTACAATCATGATAAAGTTGTATTATTTATATATTTATGAATTTTAATTGTTACAACATGACCATCATTTTAATTTCCTCATTCTTGTTTTCGGTTAAACCCATGCCAGACACATATTAAAAAGTATATATTTTAATATCTTGCATAATTAACATTTATTGCTTGTTTACCATTTATGTATGGTAGGAAATAAGCTAATATGTAATGCCAGCATGTATATACAGTAATTATGACACTCACCACTGTATCCTTTTCAACAAATTTATCTTATTTAATCGTCTGATAAAGTTGTAGTATAATACGATTTAGCTGAAATTGCAATTATATTGAGATGTATAATTCTATTGTACTGAAATAGTGAAATAGTCTGTGTAATTTTCTCTGTACTTTGCGTACACAAACTTACAATTGAAGGCCTACATTCAGACTCAACGCAAAGCTCCCACTTTTGCGCATGCATGTGAAATCGTCTGTGAATATACAAGTGTCAGTTAACCGCTGGATATATGCTGTATCTCCTGTCTGACAG
Seq C2 exon
AGAGCTGCGGTGCCATCCTCAGAACCCCGGAGTGTGAGGCTGAGGTGCACTCGGACACGGAGCGCGCGCAGCGGCAGAGGACGCGGCGGAAGCCGCGGGTTCTCTTCAGCCAGGCGCAGGTCTTCGAGCTCGAGCGGCGCTTCAAGCAGCAGCGATATTTATCGGCTCCTGAGAGAGAACATTTGGCGAGTACCCTAAAACTGACATCGACGCAGGTTAAAATTTGGTTCCAGAACCGCAGATACAAATGCAAGCGGCAGCGTCAAGACAAAACACTGGAAATGGCAGGACACCATCACCCACCACCGCCCAGGAGAGTAGCGGTGCCCGTCTTGGTGCGGGATGGAAAACCGTGTTTAACGGGATCACAGAGTTACAACACCACGTACGCGGTTAACCCAGGCCCGTACACATATAACGGGTATTCTTCTTATAACAACGCCGCTTACACAAACCCTTACAGCTGTACATACCCCAGTCTTCCTCCTCTACCTGCGAACACGTCCACTAATGCGCTGATGAGCATGAGTTTGAACAACCTCGGAACTTATTCCCAGCCGCAGACATCGCAAGGAACACCCGTGTCCGCGTGCCAAGGGACTCTGCAGGGTATCCGGGCATGGTAGTGCCAGTGCAACCCAGCCGCCTGTAAAAAAATGACAACTTAACAATATTAGCACACAGTTAGCCATGTTTTTAGGATCATGTATAGTCTATACCTTTTCAGTATAAACTTGAGAGTGAATTTCTTCTAGCAACAGTATACCATGATGGCTGAACGTGAATATTCATGGAAATTTGGACCAGCTATATATGGGCAACATATTCACCGAACATTTGACGGTCTAACTTTAGATGGTATCCATACTACTCATGAGACATTTGCTTCCTCATTCATTGCACTTATCGATGAGCAGTTATTATCTGAAATGTTACGAATATTGACAATGGTGTGTGTGACTTTGTGCAAACCTACATTGCAAAAATAAAAAAAAACGCTAAACTTTA
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000039095:ENSDART00000057094:2
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.586 A=NA C2=0.435
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0004624=Homeobox=WD(100=27.3)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TAGTGGAGAGCAGCCTTTCCC
R:
GCCGCTTGCATTTGTATCTGC
Band lengths:
354-1507
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]