DreINT0104770 @ danRer10
Intron Retention
Gene
ENSDARG00000018004 | nkx2.5
Description
NK2 homeobox 5 [Source:ZFIN;Acc:ZDB-GENE-980526-321]
Coordinates
chr14:23943996-23946789:+
Coord C1 exon
chr14:23943996-23944439
Coord A exon
chr14:23944440-23945576
Coord C2 exon
chr14:23945577-23946789
Length
1137 bp
Sequences
Splice sites
5' ss Seq
AAGGTGAGC
5' ss Score
9.6
3' ss Seq
AATAAAACAATTTTTTTCAGACA
3' ss Score
4.22
Exon sequences
Seq C1 exon
ATCTATTAGAAAGATGACTTTGGGCATATACACATAACAAATTGTCATAGGTACCCCTGATAAATCCCAACCGGATTATCCAAGTGGATCATCATTCCATGGCAATGTTCTCTAGCCAAATGACTTCCACTCCTTTCTCAGTGCGGGACATACTGAACCTGGAGCAGAATCAGGAGGACATGGTCTCCCTGGACATGTCTCAGCGGCTGGACAGCGCCCTTATTCCGACCTCATCTTGCATGCTGTCCACTTTCAAACAGGAACAGTTCATGGAAATGCCATCCGGATCCTCTCTCTTCAGCGAAGACCTTCAGGAGGACAAAGGCAACAAAATCAACTCTATTAACTTCAGTGCTTCAGGCTTTTACGCGAAGAACTTCCTAGAAATGGACTATGTTAAAGACGCAAAGACAGATGACACATTTGAAGACAAAGAGAAAAAAG
Seq A exon
GTGAGCCTTAACAGTCGGGCATTTAAACCGATATAATTGAAAATACTCTTTATTTGTTTAAACATTATGCGTTTTCCAAATATTGTGTACATTTAGGTTGAATATTACAGCCTCTTTAGGACAACTGTGCGTATATATGTTTTTATCTGTCGATTCAGCTTTGTAGTAAAAATGTTTTTGGCTAAATCTAAAATGTGAAAATGTAGCCTACTTTGAAATTTTAATTTAATAAAACTATTTTTAAAAGTGTTCTAAAACGTTAATCTGAAGTTTTAAAATAAAGATCCAAAAGGGCAGAATACCTAAGGTCACTATTTTTAGTCCATATTTAGGCGTATAACGACTATTGTCACCACCCTGAATATTCGATCTACTCATAATTACGCTATTTGCAATAATAAAATAAATAAATATAATGCTTATCATATTAGTCTATGAAGATTACTGCATTAAAATATGTAAGTCATATGCGGCTGTTTTTATTATGCTTTATAATTATACTGTAAGCCTAAACAATAAAATGTTGGAAAATTAACATGTATGACCAAAACAATTAGGCTAATTATTTTATCTGTATTATTTATGGTAATTAATCTTCGGCCCAAACTTCATTATAGCACTCAAAAAATAAGCCTGTTTGCTGCTTGTTCAAACTTTTGCTGAAACAGCACAATTCTTGTTTTGAGGGGGAAGGACAACGTAAGTGTTTTATGTTCAATCCACTTAAATTTTTAAAAACTAATAGGTTAATTTAATTCCTTCATGTTATCCCAAAACAAATCGATTGTGTGGAAGCTAACATTTAATGGTGACAGGCCTAAAGTAGCCTAATTAGTAACCTGTTTAAGAATAAAATGAATATAAATAAACTTTAATAAACAACAACAAAAAAAGTTTCGGTAAGAAATAACAGAAATATATCACAGGTCTAATAACAACAAAAACAACAACAACAACAACAACAATAATAATAATAATAATAATAATAAAATGAGTAGGCTAAATTATGACAAAATTAAGTTCTAAAGCAAAATTAAAATTCTAAGATAAACGAATGAATAAAAATATATTGTTATAACATGATTAATTTTTACCGGTGGTCAAATTTTAGTCATTCAATAAAACAATTTTTTTCAG
Seq C2 exon
ACATCGGCTGTTGTCAGGAAGACCCGGGTGAAGATCTGAAGCTGGATGATGCGGAGCGGCCCAAGCAGAGGAAGAGGAGGAAGCCTCGAGTTCTCTTCTCTCAGGCGCAGGTGTACGAGCTGGAGCGACGCTTCAAGCAGCAGAAATACTTGTCTGCACCAGAGAGAGACCACCTAGCCAATGTTCTCAAACTCACCTCCACACAGGTGAAGATCTGGTTCCAGAACAGACGATACAAGTGCAAGAGGCAGCGTCAGGATCAGACCCTGGAGATGGTGGGCATCGCACCTCCGAGACGCATCTCTGTGCCAGTTTTGGTTCGGGATGGTAAACCGTGTCTGGGAGACACGTCCACTTACAACACCTCATACAATGTGGGAATCAATCATTTCACCTACAACACCTACCCTGCGTTTAGTAATTTTCCGAGTCCAGGCAACTCGAACTACTCATGCAACTATCCGTCGAGCATGTCCAGCATCCAACCTTCACAGTCCAACAGCAACTACATGAACTTTGGTGTTGGGGATCTAAATAACGTCCAGGCTTCATTTCAATCCAGCAGTGTTCCTTCACTACATGGCATCAGAGCTTGGTGAACAAAACTACATTTACCGACAGCATTCATCTTTCTGTGGACATTTACATTCTAATGATATTTTTGATGATGAATATTATTGATTCTTGAGATATGGTTTGGCTGGGATGTTTTTTTTTTCTCTCCAAGAGACGTTTAATGTTTATGCGTGCGCATCATTTCTTTCAAAAACTGTCTGAATAATTTGCTTGCACTTGAGTTCAATTATGAGATTAACAGCACGTGGAAAATGTAGGCAGAATATTTATATTTTCACCAAATGTATGATGAGGCCTGTGCTTAAATCTCTTGCGAAATTACCAGGTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTGAGTTCTTTCTTTCTTGAGTTCTTTTTTTTCTTAATCAGTTAATTTTTTTTGTAAACGTTGCTTAATAAAGACCTGTATTATTGATAACCACAGTGCATCAAGGATTTTTTAACTTATTTTTTCCTTTGTGCGGAAAGTGAGCTGCAGCACGAACACGGCTCCGACTTTACCTTTTGTTAAAATAGGCTTTGCCAGTGTAAGTTTGATATGTACATTTGTTGAAGAAAAACAATAAAGGATCTTCTAGAACGTA
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000018004:ENSDART00000022377:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.190 A=NA C2=0.141
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0004624=Homeobox=WD(100=28.5)
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:
GCCATCCGGATCCTCTCTCTT
R:
GGCTAGGTGGTCTCTCTCTGG
Band lengths:
346-1483
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]