DreINT0084789 @ danRer10
Intron Retention
Gene
ENSDARG00000029881 | kcnh2a
Description
potassium voltage-gated channel, subfamily H (eag-related), member 2a [Source:ZFIN;Acc:ZDB-GENE-070912-699]
Coordinates
chr2:24504173-24505760:+
Coord C1 exon
chr2:24504173-24504425
Coord A exon
chr2:24504426-24505566
Coord C2 exon
chr2:24505567-24505760
Length
1141 bp
Sequences
Splice sites
5' ss Seq
TAGGTAAAG
5' ss Score
6.93
3' ss Seq
TTTTGGTCTATATTTTTCAGGCA
3' ss Score
8.73
Exon sequences
Seq C1 exon
GTGCTGAAGGGTTTTCCTGAGTGCTTACAGGCTGACATCTGTTTGCATCTGAATCGTACACTGCTGCAGAGCTGTAAAGCTTTCAAGGGTTCCTCCAAAGGCTGCTTGCGTGCTCTGGCTATGAAGTTTAAGACTACTCACGCTCCTCCAGGAGACACCTTGGTCCATGCTGGAGATGTGATTTCAGCGCTATACTTCATATCTCGGGGCTCCATCGAGATTTTAAAGGGAGATGTAGTTGTGGCTATTTTAG
Seq A exon
GTAAAGGAGATTTTGGGTTGATTTTATTGTAATTATATCTGGATGTCAGGGCATTTTCAAACTTTTTGATGTCCCTAACCCTTACCCAGACACTCCCCACCCAATAATAATCTAATCAGAGATGTTTGGTATGTACTGTAGTTGCAAAGATATTCAGATGGAAATCTGATATAGCATATATGATCATATCAACCGTATGTAACATTATCGATGAATGTGTATGTACAGTGGTCAGCATGATTGAGTATTAAACAAAACAGATGTATTAAACAGATATATTTATTAAAATAATATTTTAGTCACCAAATATATTTAGAAACTGAAAGATATTACAATAAATTTCAAGCAAAGTATTACAAAAAAATACAACCTACAAAATTTCAACAAAAAGTTTAATTTTTTTTTTTTTTTGCTCCTTTTATTTTTTTCTCTTTTTAAATTTGTATTTAATATAATTAAATTAATAATTTCTATAACATATAATTTTGGTTGTACTAGTTTGTGGACCATTATTGTAAGTTATTATGTTTGATAAGCTCTATAATTGGCTTCAGTACTGACTAATGTATATGCACAAATAGAATATTTTGTCTAGCTACCTATTAAATATATGAATTTAAAAGATAGATTTGTGAGGGATGTACTCAGGGACGGACTTTTTTAATACTTAAAAATTTTCACATTTTTTTTCCCTTAATTGAATGCTTATTTTTTTTTACCTTCATACTAAATGACTATTTATGGGGTTCAGGGTCAAATATAAGTTTCATATTTATAACAAAGTATCAAAATTTTGATATATTTACCAAATTTCAGATCTCTGTATGGGTAGTATGGGCATTAAAATCAAGTGTAACTCTTCTTTTATTTACAATTATGCGTTTAATGGTGTTTCAAACCTCAAGTTTTCCTTGTGTGGCTCCATCTTGTGGACATTTTGCTATTTTGTTTTCTGTCATGTTCATGTTTTTTTAATGGCATGCAGCGCCACCTGCTGTTGATTTCAAATATTTTCACATTTCTAGTGCTGTATTCACAATAACACGTTACATACTAACATATTCCTGAATAACTTCCATACCATGTCCATACTATCTGACATAATTTAGGCATTAAATGTCTTTTGGTCTATATTTTTCAG
Seq C2 exon
GCAAGAATGATATATTTGGAGAGCCCATTAACTCATATGCTCGTCCTGGAAAGTCAAGTGCAGATGTGAGAGCACTTACGTACTGTGACCTGCACAAAATCCACAGAGATGATGTCCTGGAGGTCTTGGAAATGTATCCAGAGTTCTCTGACTACTTTTGGAGCAATCTGGAAATCACTTTTAATTTGAGAGAC
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000029881:ENSDART00000024058:9
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:
PF0002724=cNMP_binding=PU(45.5=47.1)
A:
NA
C2:
PF0002724=cNMP_binding=PD(53.4=72.3)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
ACAGGCTGACATCTGTTTGCA
R:
TCCAAGACCTCCAGGACATCA
Band lengths:
357-1498
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]