HsaINT0084704 @ hg19
Intron Retention
Gene
ENSG00000107147 | KCNT1
Description
potassium channel, subfamily T, member 1 [Source:HGNC Symbol;Acc:18865]
Coordinates
chr9:138662703-138664795:+
Coord C1 exon
chr9:138662703-138662941
Coord A exon
chr9:138662942-138664560
Coord C2 exon
chr9:138664561-138664795
Length
1619 bp
Sequences
Splice sites
5' ss Seq
TGGGTGAGC
5' ss Score
7.23
3' ss Seq
AGCACAGGGCTCTCTTCCAGGGA
3' ss Score
4.18
Exon sequences
Seq C1 exon
GTATGGCGTGTGCCTCATCGGGCTGAAGCGGGAGGACAACAAGAGCATCCTGCTGAACCCGGGGCCCCGGCACATCCTGGCCGCCTCTGACACCTGCTTCTACATCAACATCACCAAGGAGGAGAACTCGGCCTTCATCTTCAAGCAGGAGGAGAAGCGGAAGAAGAGGGCCTTCTCGGGGCAGGGGCTGCACGAGGGTCCGGCCCGCCTGCCCGTGCACAGCATCATCGCCTCCATGG
Seq A exon
GTGAGCCGGGACAGGCGCGCGGGACTCCCTGGGCCTGCTCCTTTGGCGGGAGACCAGGCGGGACACCGGCAGGTGACCAGGTGGGATGGGAGACCAGGCAGGACAGGGGGAGGTGACCAGGTGGGACAGGAGACCAGGCAGGACAGGGGCAGGTGACCAGGTGGGACGGGAGACCAGGCAGGGCGGGAGACCAGGTGGGACAGGAGACCAGACCGGGCAGGGCAGGAGACCAGGCCAATGTGGCCCCCAGACCCAGTTCCTCTTGGCCTATGCCTCCAACCTTGGACAGGTGGAGTCTCTCTGGGCCTGTTTTTGAATCTGTCAAACAGGTGTCCCCGCCTTCCTGTGGCCACCTTTGTGGGCATTGCTCACTGTGTCCAAGTGCCTGTCCAAGTGGGGCCGCCCACAGGACCGGTTGGCAGCTCAACCGGAGGCTCCTGGTGGTCCCATCAGCCCGGAGGGTCTGCTTCACGTGTGTCCCTCAAACAGTCGGGAGTCCTGACGTCCACTGGGGCCAGGAGTTGGCGGAATGAGGTCGCAGTGGCCGAGGGCTTTGGCCTCTTCTCGTGCCTTCAGGGATCCTCCCGGGGAGCCGCTTACCAGACAGGGTCAGGCTGCCTCTGAGCAGGTGGAGGCCCATGGCCCCTAGGGCACCACCCATAGTGGTGTTGCCCCCTCCCCAGCCAGGCCTTCCTGGGGGACAGTTAGGGAGCAGGGCCAGGCCAGGAAGCCACTCAGGCCACAGACCCACAGCCGGGCCAGCATGTTGCCACCTCCGTACAGTGGCCCAGGCAGAGGCTGACCCTATGGGGCACCCCAGCACGCCCACCCTGGGGTGTTGTTACACGGTGGCTGCTGGGGCACCAGGTGGTTCAGTGCAGTGGGGCACAGTCTCCAAGACCCAGAGGGCCCTGGGGTTTGGAGACGTGCCGATGCGGAGCCCACCACCTGCCAGACCCCGCAGGTTCCCGGCCGCCGTCTACGGCAGCTCACTCGGGGGGCCGGGCCTGGCCGCAGGGCACTGGGGAGGCAGGCTGCTGCTGCCTAGCCACACCTCCACCTTCACCTGCGCAGTAGGCACTCTGCCCCCAGGTGGCTTCCAGGAAACCAGGGTGACTCGGGCAACCCTCACTGTACCCACAGAGGCCCTGGGCCATACCTAGAGGTCCACAACCCCCATCTGGCAGCCTGGGGTGGTGCAGGAGTGGCAGAGTCTGCTCCCACAGGCACTGAGTCACCCAGCTGCTCCCCACCTGGCCCCATCCACCAGGCAGCCTGACCAGCTGCACAGGCCCCTAAGGCTGAGACCCCCGAGCCCAGAATCAGCCAACCCCCTCCTCAGGCATCTGGTGCTGAGGCCACAGCAGCTGGCCTGGGTGGCACCGATGGGGCACTGGGGCCCCCTGGGTCTTCGCTCAACATCATCGCCACCCCAGAGGCCACTGTCCCTGTTGTATGGAGGGGGAAACTGAGGCATAGATTGAAGCTCCTCAGCTGGAGCACAGGAGCCAGGCCATGACAGGGTCTCCAGAGCTGACTGTGTTCACCTGAGCTCTGGGAACTCGCCGCCCATGGAGGGTGGGAGTCGGGCTGTGGCCAAGCACAGGGCTCTCTTCCAG
Seq C2 exon
GGACAGTGGCCATGGACCTGCAGGGCACAGAGCACCGGCCTACGCAGAGCGGCGGTGGGGGCGGGGGCAGCAAGCTGGCACTGCCCACGGAGAACGGCTCGGGCAGCCGGCGGCCCAGCATCGCGCCCGTCCTGGAACTGGCCGACAGCTCAGCCCTGCTGCCCTGCGACCTGCTGAGCGACCAGTCGGAGGATGAGGTGACGCCGTCGGACGACGAGGGGCTCTCCGTGGTAGA
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000107147-KCNT1:NM_020822:18
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.108 A=NA C2=0.605
Domain overlap (PFAM):
C1:
PF0349313=BK_channel_a=PD(8.5=11.1)
A:
NA
C2:
NO
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:
GCCTCTGACACCTGCTTCTAC
R:
CACCTCATCCTCCGACTGGTC
Band lengths:
357-1976
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)