HsaINT0084715 @ hg19
Intron Retention
Gene
ENSG00000107147 | KCNT1
Description
potassium channel, subfamily T, member 1 [Source:HGNC Symbol;Acc:18865]
Coordinates
chr9:138677156-138678367:+
Coord C1 exon
chr9:138677156-138677176
Coord A exon
chr9:138677177-138678042
Coord C2 exon
chr9:138678043-138678367
Length
866 bp
Sequences
Splice sites
5' ss Seq
CAGGTAAGC
5' ss Score
9.88
3' ss Seq
CCCTGCCCTGCCCTGCCCAGTCC
3' ss Score
7.68
Exon sequences
Seq C1 exon
CCCCACGACCTCAGAGCCCAG
Seq A exon
GTAAGCAACCCCTCCGTGCCCACGCAGCTTCTGCGGAGCACCAGAACATCGCAGCTTCACATGGAGAAGCCTGCCAGGCCCCACCCACCCACCCACCCACAGGGCCCTGGGAAAGCCGAGGCAGGAGCGGGTCCCACGGATGTGTCGGCCCCAGCACGGCTCAGAGAAGGCTGTTGACACTCACTCCCTCCTGCACTGGTGGTGGGGAAGCTGAGGCCTGGGGGGAGTAGCCTGTGAGTTTGGACACCAGGTGCACCCCCGCCCCCTCCCAGGCCCCACCAAGGCAGGCAGCCCCCATGCCCATCTGGCCTGACCAGCCCCCAGCCTCCCAGGCCTTTCTGAAGGTGCCACCCAGGTGGGATGCCTACCTCTTCCCAGCACCCCACGACCCACAGGCTCTGGCACCCCACGTTCCCCAGGTTCGGGGCCTCCAAAGGGTGTGTTTGCAAGAGGGATCAGGGCTCATCTGCAGATGGAGAAATTGACACGCAGAGGGGGTGACCTCTCAGGGCAAGGCCAGGATGTGCTGGGGTCCAGATGGGTCCCAGGCCGGACCCACAGAAATAAGGGCTCAGAGAGGCGAAGGGAGCTGCCCTCAGCAGCCTGGCGAATCCCTTGACCAGGCCCGGGCAGGGTGGGTGGCCCGGCGATCTGTGCTCAGGAGGAAACCAGGCACATTCTTTCCAGAGGAGGAAGGCACATGCACCCTGGGGTCTGTCGTCGTCCTCTTCCCTAACACCCCCAGCTGCTCCCACGCAGGCCCCAAGCTGCAGAGCCCACACCTCTTCCTAAGCCCCTGCCCCAAAGCCCGCGACCCTCCCGGCAGCCTCACCCCTCCCCGCCCTGCCCTGCCCTGCCCTGCCCAG
Seq C2 exon
TCCCAGATCTCGGTGAACGTGGAGGACTGTGAGGACACACGGGAAGTGAAGGGGCCCTGGGGCTCCCGCGCTGGCACCGGAGGCAGCTCCCAGGGCCGCCACACGGGCGGCGGTGACCCCGCAGAGCACCCACTGCTACGGCGCAAGAGCCTGCAGTGGGCCCGGAGGCTGAGCCGCAAGGCGCCCAAGCAGGCAGGCCGGGCGGCGGCCGCGGAGTGGATCAGCCAGCAGCGCCTCAGCCTGTACCGGCGCTCTGAGCGCCAGGAGCTCTCCGAGCTGGTGAAGAACCGCATGAAGCACCTGGGGCTGCCCACCACCGGCTACG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000107147-KCNT1:NM_020822:28
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.143 A=NA C2=0.550
Domain overlap (PFAM):
C1:
NO
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:
CCACGACCTCAGAGCCCA
R:
CAGCCCCAGGTGCTTCATG
Band lengths:
328-1194
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Genotype-Tissue Expression Project (GTEx)
- 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)