HsaINT0084342 @ hg19
Intron Retention
Gene
ENSG00000089558 | KCNH4
Description
potassium voltage-gated channel, subfamily H (eag-related), member 4 [Source:HGNC Symbol;Acc:6253]
Coordinates
chr17:40327597-40328315:-
Coord C1 exon
chr17:40328072-40328315
Coord A exon
chr17:40327755-40328071
Coord C2 exon
chr17:40327597-40327754
Length
317 bp
Sequences
Splice sites
5' ss Seq
TAGGTCAGA
5' ss Score
4.42
3' ss Seq
ATAGCCTCTTGCACCCCCAGATA
3' ss Score
7.86
Exon sequences
Seq C1 exon
AACGTGTTTGAGCCAAAGCCATCAGTGCCCGAGTACAAGGTGGCCTCCGTGGGGGGGTCTCGCTGCCTCCTCCTCCACTACAGCGTCTCCAAGGCCATCTGGGACGGCCTTATCCTCCTTGCCACCTTCTACGTTGCGGTCACCGTCCCCTACAATGTCTGTTTCTCGGGTGACGATGACACCCCCATCACTTCGCGACACACCCTTGTCAGCGACATCGCCGTGGAAATGCTCTTCATCCTAG
Seq A exon
GTCAGACCTTCTGCCTCACCCACCCTGGTGGGTCGGCTGGGGGGATCCACTTGGCCAAGCCTCACCCACTCCTGGGGCCCACATGACCCAGACATTCAGAGCCCCTTCCTTTCTGCATCTTTAAGTCCCAATGGCCCATGTGTCCTGCTCCCCGCAGCCTTCAGCCTTGTAACCTATCCTCCCTAAGGACCAGCCAGAAGCCCAATCTATCTCTCCATGCCTGCCTCCTCCTCCAGTCTCCAAAGCTTGTTCCCAGCTTTGTCGGTTTCTTGACCCCTTTGCCAAGGCCCCCCAGTAATAGCCTCTTGCACCCCCAG
Seq C2 exon
ATATCATCCTGAACTTCCGCACCACCTATGTGTCCCAGTCCGGCCAGGTAATCTCTGCTCCTCGTTCCATTGGCCTCCACTACCTGGCCACCTGGTTCTTCATCGACCTTATTGCTGCTCTGCCCTTTGACCTGCTTTACATCTTCAACATCACCGTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000089558-KCNH4:NM_012285:5
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.012 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0052026=Ion_trans=PU(5.7=14.6)
A:
NA
C2:
PF0052026=Ion_trans=FE(24.8=100)
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:
CGTGTTTGAGCCAAAGCCATC
R:
GATGAAGAACCAGGTGGCCAG
Band lengths:
346-663
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)