HsaINT0084339 @ hg19
Intron Retention
Gene
ENSG00000089558 | KCNH4
Description
potassium voltage-gated channel, subfamily H (eag-related), member 4 [Source:HGNC Symbol;Acc:6253]
Coordinates
chr17:40330349-40331044:-
Coord C1 exon
chr17:40330811-40331044
Coord A exon
chr17:40330496-40330810
Coord C2 exon
chr17:40330349-40330495
Length
315 bp
Sequences
Splice sites
5' ss Seq
ATGGTGAGG
5' ss Score
7.61
3' ss Seq
CCCTCTCTCCATGCCTACAGGCT
3' ss Score
9.58
Exon sequences
Seq C1 exon
ACAGCAACTTCCTGCTGGCCAACGCACAGGGCACACGGGGCTTTCCCATCGTCTACTGCTCCGACGGCTTCTGCGAGCTCACAGGCTACGGTCGCACCGAGGTCATGCAGAAGACCTGCAGCTGCCGTTTCCTCTACGGCCCAGAGACCAGTGAGCCAGCCCTGCAGCGTCTGCACAAAGCCCTGGAGGGCCACCAGGAGCACCGGGCTGAAATCTGCTTCTACCGCAAGGATG
Seq A exon
GTGAGGGGGCTCACCCCACCCTGCAGCTCTGCCTAGACCCCTAGCCTTATCCAGAGGGCACTGGGCACAGTAGGAGTCTGAGTGCTTGTCCCCACACTGCCAAAAGCTGACTGTGACGGAGCGTATCCCTGACCTCTCTGGTCCTGGGTTCCCCCATTTGAAAGATGAAGGAATCGGCTGACAGAATCTCTGAGGTTCCTTTTGGTTCTTGCTTTGCCAAGCTCTTAACTATGTCTAGGAGGATGAGAGGGATGAGGAGAAAGGCATGCCATGGGGCTGCCCATGCTCCTCCCTTCCCTCTCTCCATGCCTACAG
Seq C2 exon
GCTCAGCCTTTTGGTGCCTCCTGGACATGATGCCCATCAAGAATGAGATGGGGGAGGTCGTGCTGTTCCTCTTTTCCTTCAAGGATATCACTCAGAGTGGAAGCCCAGGACTTGGCCCCCAAGGAGGCCGCGGGGACAGTAATCACG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000089558-KCNH4:NM_012285:2
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.076 A=NA C2=0.300
Domain overlap (PFAM):
C1:
PF134261=PAS_9=PU(70.6=97.5)
A:
NA
C2:
PF134261=PAS_9=PD(28.4=62.0)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GGCTTTCCCATCGTCTACTGC
R:
CGTGATTACTGTCCCCGCG
Band lengths:
343-658
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Autistic and control brains
- Pre-implantation embryo development
Other AS DBs:
FasterDB (Includes CLIP-seq data)
AS-ALPS (AS-induced ALteration of Protein Structure, links to PINs)
APPRIS (Selection of principal isoform)
DEU primates (Only for human)