DreINT0084814 @ danRer10
Intron Retention
Gene
ENSDARG00000062565 | kcnh4a
Description
potassium voltage-gated channel, subfamily H (eag-related), member 4a [Source:ZFIN;Acc:ZDB-GENE-131125-34]
Coordinates
chr3:17428539-17430816:+
Coord C1 exon
chr3:17428539-17428800
Coord A exon
chr3:17428801-17430661
Coord C2 exon
chr3:17430662-17430816
Length
1861 bp
Sequences
Splice sites
5' ss Seq
TCGGTATGC
5' ss Score
7.85
3' ss Seq
ATACATTTTTCTTTTTCTAGATA
3' ss Score
8.85
Exon sequences
Seq C1 exon
AATGTGTTTTCACAGCCAACTCTCCCCGAATACAAGGTGGCGTCGGTGCAGAAATCTCGCTTCATTTTGCTTCATTACAGCGTGTGCAAGGCCATGTGGGATTGGTTGATCCTCCTTGCCACATTTTACGTGGCTGTCACCGTCCCCTACAACGTCTGCTTCTCCACCCCAGACGACAGCCAACTCGACAGCCCGGATTGCGACTCCAGCTCCAGGACCACCATCGTCAGTGATATAGCTGTGGAGATGCTCTTCATCCTCG
Seq A exon
GTATGCTGTTTTCAGGGCTCATTTCCACCTCTGTTCCAATTTTAAACAGTGTTAACTTCTGACATCCGCTGAGCTCTTTCACCTTAAACATGTTAGCAAAGTGAAACATCACACCTTCAGCTCCTACTGAAACTATCTTTCAAATCCACACTGCCAATATGATCTGGGTTTTAGACAAAAAAATTAAGAGATTTAATGAATAATAAGTTTACCTTTTCAGGCCTCATGATCAAGATTTAGACCATTTTGAGTCACACTTGGGTAATTCAGTGAATTGCTTTGACTGGAGCACTGGATCATTTGAATCAGGGACTTGTTAACTAGAGACTCATTTTCACCGAATCATTTATATCAGTGACTTGTTAGCTGGAGATTTGTTCTGACCAGATCATAGTGAGTCATTAACTGGAGATTAATTTGAGACTCATTATGACCAAATATTTCCAATTAGTGAATCATTGTGATTCATTGTGACTGAATCATTTGAATCAGTATGTTATTTACTGGAGATTCTGACCAGATAATTTAAATTAATGAGTCCTTACCTGGAGATTTGTCCTGATCGGATCATTTGAATCAGTGTGTCATTAACCGAGGACTCATTATGACTAATTATTCCAATTAATGAATCATTAACTGGAGATTCATTCTGATCAAGTCATTTGAATCAGCGTGTCATCGCCTGGAGACTCTTTCTTACCAATTAATTCCAATTAGTGAGTCAGTAACTGAACATTCATTCTGATCAAATCATTTGAATCAGTGTGTTATTAACTGGAGATTTGTTTTGACTAAATATTTCCAATTAGTGAATCATTCACTGGAGATTTATTCTAATTGAATCATTTGAATCAGTTTGTCATTACCTGGAGACTCATTATGATCAAATATGTCCAATTAGTGAATCATTAGCTGGAGATTCATTCTGATTGAATCAGTTGAAACAGTTTGTTATTAACTGGAGATTTGTTCTGATCAAATATTTCCAATTAGTGAATCATTAACTGGAGATTCATCCTGATCGGATCATTTAAATCAGTGTGTCAATTACTGAACACTCATTATGACCAAATTATTAGACTAGTTAGTGAGTCATTGAGATTTCTTCTGAGTGAAAAAAGATAAAAGCACGAGTCAAGTCCAGAATTAATAGTTGCATAAAAGATACAGAGCTAAAAAAATTAATACAGTCTACGAAAAATGTGTGCAAATTTTGTGTTTACAGTACAAGAAAGTGTGTGGAAATACAGACAGTAAACAATGTAAACACGGTAAAATACACTACTCGACATTATAATTTAGAAACAATATAATATGTAGAGTGTGGTTATCTGTACAGTATATAATGCTATCATTTTGAAAGATACTCTGCTTTGAAATGTATTAAAATAATAGTTTCCCAAAATAAAAATATTTCCTAAAATCAATTTGAATCAATAATTTTTAATCTTTTTTTTTTGGCATTCTGCCATTTTTTTAGATGGCAAAAGAGAGCTGTGTTGGCATAAACTGTTAGTAAATCTTGCCATAAATCTCTCTTATTAAGAAAATGCTCCACTGTGACCCGAAGCCAGTGGTAATTTTAATAAACCCCATGAACACAGATGCGGTAAAAGAATTAATTGATGGAACTAAATGTACCGCTTAATAAAAATCTGCACAGAACAAGAATCATGAATATTTATTGAGTCCAGCATGTACTGTACAAGGCTTCATCACTCTAATTAACATGTTTTTAATATTCATGCATCCGCAGTCAATATTTGCCTAGAAAGAACACTGTTTATGATTATTATTGGTATAGATTTTTTTAAATGCTGTGAATCAAGTAATAATCTTTTATACATTTTTCTTTTTCTAG
Seq C2 exon
ATATTATACTGAATTTCCGAACCACTTATGTTGGCCCTGCGGGTCAGGTGGTTTATGATACTCGCTCGATTTGTTTGCACTACTGTACTACCTGGTTCATCCTGGACCTCATCGCTGCTCTGCCCTTTGACCTGCTCTATTTATTCAACATCTCA
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000062565:ENSDART00000153763:5
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0052026=Ion_trans=PU(5.7=13.6)
A:
NA
C2:
PF0052026=Ion_trans=FE(24.4=100),PF068148=Lung_7-TM_R=PU(25.0=48.1)
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:
CGGTGCAGAAATCTCGCTTCA
R:
TAGAGCAGGTCAAAGGGCAGA
Band lengths:
358-2219
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]