HsaINT0084702 @ hg19
Intron Retention
Gene
ENSG00000107147 | KCNT1
Description
potassium channel, subfamily T, member 1 [Source:HGNC Symbol;Acc:18865]
Coordinates
chr9:138661793-138662293:+
Coord C1 exon
chr9:138661793-138661901
Coord A exon
chr9:138661902-138662143
Coord C2 exon
chr9:138662144-138662293
Length
242 bp
Sequences
Splice sites
5' ss Seq
CCAGTGAGT
5' ss Score
8.28
3' ss Seq
GGCCCCGCCCTGGCCCACAGGGA
3' ss Score
7.64
Exon sequences
Seq C1 exon
ACCACGTGGTGTGTGAGGAGGAGTGCAAGTACGCCATGCTGGCGCTGAACTGCATCTGCCCGGCGACCTCCACCCTCATCACCCTGCTGGTGCACACGTCCCGCGGCCA
Seq A exon
GTGAGTGCCCCGTGCCCCGGGGGACCGACCTCCATGGCGGGGCCGGCGCAGGGAGACAACGCAGGGCCTGCTTGGGGGCGGGGATGGGCTTCCCAGAGGAGGGGCACATGGCGGGCAAAAGTCCTGCATAGGGAGGGGATCCATGCCAGGGGAAGCAGAGGGGGGCACCTGCAGACCCAGCCGGGGAGAAGGGGCAGCCATGGCCGAGGGTGACGCTCCCCTGGCCCCGCCCTGGCCCACAG
Seq C2 exon
GGAGGGACAGGAGTCTCCGGAGCAGTGGCAGCGCATGTATGGGCGCTGCTCCGGCAACGAGGTGTACCACATCCGCATGGGTGACAGCAAGTTCTTCCGCGAGTACGAGGGCAAGAGCTTCACCTACGCGGCCTTCCACGCCCACAAGAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000107147-KCNT1:NM_020822:16
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=0.098
Domain overlap (PFAM):
C1:
PF0349313=BK_channel_a=FE(34.0=100)
A:
NA
C2:
PF0349313=BK_channel_a=FE(47.2=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GGTGTGTGAGGAGGAGTGCAA
R:
TTCTTGTGGGCGTGGAAGG
Band lengths:
252-494
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)