HsaINT0084696 @ hg19
Intron Retention
Gene
ENSG00000107147 | KCNT1
Description
potassium channel, subfamily T, member 1 [Source:HGNC Symbol;Acc:18865]
Coordinates
chr9:138650260-138651705:+
Coord C1 exon
chr9:138650260-138650354
Coord A exon
chr9:138650355-138651524
Coord C2 exon
chr9:138651525-138651705
Length
1170 bp
Sequences
Splice sites
5' ss Seq
GGGGTGAGT
5' ss Score
7.93
3' ss Seq
CTCACTGCCAGGGGTTGCAGGAC
3' ss Score
-1.53
Exon sequences
Seq C1 exon
AATGACTTCCACCGTGCCATCCTGCGGACACAGTCAGCCATGTTCAACCAGGTCCTCATCCTCTTCTGCACCCTGCTGTGCCTCGTTTTCACGGG
Seq A exon
GTGAGTGCCGGCCGTCAGTGTGAGCACCCCAGGACGTTGGGAGGGCCCGAGAGGCAAGCAGGGCCGGGCGAGGGGATACAGATGCCTATGTCCAAGCTATCGGGGCAGAAAAGGCCACAGTGCCTGGGCTGCGGGTGTCGGGCCACCAAGCTGGGACTGAGGTCAGGAGGCAGCTCCAAGCCCACGTCCCCAGTACACGAGCAGCCCTGCAGCCCGACTCCTCCAAGGACAGAGATACCCAGATCTGGCTTCCTGGTCTATGCCATGGACGTAGAGAAGGGGACTGGCCCCTAGGCCAGGTGGGGTCTCTTGGCTGAGGCCCAGCTGAAAGCAGGGTCTGGAGGCAGCCAGGGTAAAGGTGGGGGTGCCCAGAGCTGCGAGGGCCTCCAGCCCACCCAGGCATGCCCACTGTGCCCACCTGCCTGTGTCCTCGTGGAGGGCTCCATGTTGCTGCTCTGCCTTGGGTCCCAGCGAGGCCTGGTCACCACTTCCCGTCCCCAGGCAGGGATGTCAGGCAAGCACTGTGCCCTGGGGGAGGGAGAGTGCCCTGCGTTTCCCGCCTCCCTTCCCCCCTGCCCCTCATGACAGACTGACAGACACAGAGCTGAGTGGGCAGATTGGGGCATCCATGAGGATAGCATCTGGGACCTGGCGGCGACCCCAGCCCTGCCCATTAGACCTCCCAGCCTCAGGCCTGGGCGCTTGTCTGGCTGTGCCGGGCAGAGGCCTGAGTGTGGTGGGTAAAGGGGCAAGGCTCTGAGATGGGGGTAGAGGGCCAGACCCCAGGCCCACCCCTGTGTCACCCAAGCCCACGCTGATGACACAGCCCTGCATCCCCTGCTCCCAGAGAATGTTCCAGGGACCTAGGAGAGAGCCACCCGGCAGGCAGGGAGGCTCCGGGGAATTCGCCGTGAACAGAGGCCGCCATGCTGTGGCCAAGCTGCATTGTCAGCCAGCGTCAGGCAGGAGGTGGCTCCGGCAGAGCTTGGGGACAGATGGGCAGGGCTGAGGGCCTGATGCCACCCAGCTGTCAGGAGGGCGGGGCTCGCCTGGTGATGCACAGCTCAGTCTCCTGGGCAGTGAGGGTCCCGTGGGCAGGCAGGATCTCTGAGGGGCCACGGCCCCCCAGCTCCTGGGCCCCAGGCCGCCCCTCACTGCCAGGGGTTGCAG
Seq C2 exon
GACCTGCGGCATCCAGCACCTGGAGCGGGCGGGCGAGAACCTGTCCCTCCTGACCTCCTTCTACTTCTGCATCGTCACCTTCTCCACCGTGGGCTACGGTGACGTCACGCCCAAGATCTGGCCATCGCAGCTGCTGGTGGTCATCATGATCTGCGTGGCCCTCGTGGTGCTCCCACTGCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000107147-KCNT1:NM_020822:10
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=0.000
Domain overlap (PFAM):
C1:
PF0788511=Ion_trans_2=PU(12.5=31.2)
A:
NA
C2:
PF0788511=Ion_trans_2=PD(79.1=96.4)
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:
AATGACTTCCACCGTGCCATC
R:
GCCACGCAGATCATGATGACC
Band lengths:
254-1424
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)