HsaINT0084332 @ hg19
Intron Retention
Gene
ENSG00000089558 | KCNH4
Description
potassium voltage-gated channel, subfamily H (eag-related), member 4 [Source:HGNC Symbol;Acc:6253]
Coordinates
chr17:40317467-40318564:-
Coord C1 exon
chr17:40318315-40318564
Coord A exon
chr17:40317712-40318314
Coord C2 exon
chr17:40317467-40317711
Length
603 bp
Sequences
Splice sites
5' ss Seq
TGGGTAAGG
5' ss Score
9.08
3' ss Seq
TCCCCATCCCTTACCTACAGGGA
3' ss Score
10.21
Exon sequences
Seq C1 exon
TTACTGCGTGACTTCCCAGACGAGCTGAGAGCTGACATTGCTATGCACCTGAATCGGGAGATCCTGCAGCTGCCGTTGTTCGGGGCAGCGAGCAGGGGCTGCCTGCGGGCCCTATCGCTGCACATCAAGACCTCGTTCTGCGCTCCGGGCGAGTACCTGTTGCGCCGTGGGGATGCCCTGCAGGCACATTACTATGTCTGCTCCGGCTCGCTTGAGGTGCTCCGAGACAACATGGTGCTGGCCATCCTGG
Seq A exon
GTAAGGACACCGTCACCCTCTACTACCTACCCTGGAACCACCCCCCGCAACCCCCACTGAGGACTTGGGAATGGCCAGGATTCTAGGGAATGGGATACCCCTCGTGGATACCTACAGTTCCTGCTGAGGAGTACTCTCTCGGTCCCTCCGCCCTACGACCATCGCCTTTAGACAATTCCCCCTAATCCCCTTGGGCATCCCTCAACCCATCAACCCTTCCCGGTGACTGTCCCCCAGCTCAATTGATCCTTTCCCATTGCTCCACTTCCCAACCCCATTGACCTTTCCCCAGTGACCCTAAACTCCATTCACTTTTACCCTCTAACTGACCTGACCCCTCCGGCCATTGTGATTTTTATCACCCAATTCCACTGATCGTTCCTCTGGCCCTACTCACTCCCACTGACTGTCTCCCAGCCTTACCAGTCATTCTGCACTGACCTTTTCCCAATTCCATTGGTTATTTCCACCAATCCCATTGACTGGCCCACCTTCAACCATCCTTCAAACACACTGACCACCCCTCAAATCCACTGAGCACCTCCAGCTGATATCCTTTCGTTCTCACTGCCCCAGCTGACTGTCCCCATCCCTTACCTACAG
Seq C2 exon
GGAAGGGGGACCTGATTGGAGCAGATATCCCTGAGCCGGGGCAGGAGCCTGGGTTGGGAGCAGACCCAAACTTCGTGCTAAAGACCAGTGCTGATGTGAAAGCTCTGACCTACTGTGGCCTGCAGCAGCTGAGCAGCCGAGGGCTGGCTGAGGTCCTGAGGCTCTATCCTGAGTATGGGGCTGCCTTCCGGGCTGGCCTGCCCCGGGACCTCACCTTCAACCTGCGCCAGGGCTCTGACACCAGT
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000089558-KCNH4:NM_012285:10
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.146
Domain overlap (PFAM):
C1:
PF0002724=cNMP_binding=PU(40.8=47.6)
A:
NA
C2:
PF0002724=cNMP_binding=PD(58.2=69.5)
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:
ACATCAAGACCTCGTTCTGCG
R:
CGCAGGTTGAAGGTGAGGTC
Band lengths:
355-958
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)