HsaINT0084731 @ hg19
Intron Retention
Gene
ENSG00000162687 | KCNT2
Description
potassium channel, subfamily T, member 2 [Source:HGNC Symbol;Acc:18866]
Coordinates
chr1:196309471-196311358:-
Coord C1 exon
chr1:196311209-196311358
Coord A exon
chr1:196309701-196311208
Coord C2 exon
chr1:196309471-196309700
Length
1508 bp
Sequences
Splice sites
5' ss Seq
AAAGTATGT
5' ss Score
6.93
3' ss Seq
CTCTTTTTTTTTAAATTAAGGTT
3' ss Score
7.78
Exon sequences
Seq C1 exon
AGAAGGCCAGCAATCGCCAGAACAATGGCAGAAGATGTACGGTAGATGCTCCGGGAATGAAGTCTACCACATTGTTTTGGAAGAAAGTACATTTTTTGCTGAATATGAAGGAAAGAGTTTTACATATGCCTCTTTCCATGCACACAAAAA
Seq A exon
GTATGTTTCTGCCTCAGAGAAAAATTAAAATATCAATCAGTCAAGCATATCATGTGAAAATAGTTTTCAAAAATAGAATGCATATTGTGTTCATGTGTTTAGGCATTCCGGAATTTTTGTCACAATATTCCCCAATGTTGAAACATTTGAACCCTGGTGTCTGTATGGTCTCTATAAGACAGTCAGGAGTAAATTATAATTTAGTAGGAATATTTCATTTAGCCACTTTTAAAGTCTTTTTAAAATATTTTAATCCATTAAGAATTTACATACATATGAAAATCTTCTTCACAGATCTGAATTTTAAGATGTTGATTAGGAACTAAAACAAAGTAACACTAATATTTCTAAAAACTGTACATTTGAAAAAAAAATCTCTGATGGTGGCCCTTGTTTTGGCCTGAGAAATAAGTTAAAAAATAAATAAAACTACCTTCCAATTCAAACATAGAACTTTTTTTTTCTTTTCCTTTTTGGAAAAAAAAAGGATTTACTTAAGAAGTAAAAATGTATGTATATAATGAAAATAACATATTATCTGTATTAAATGTTTTAATGTGACACATTTTGGAGGATTTACAATATACGTATATAGTCTACTAACTAATCTATTATGTAATGTACAGGAACCCCCAACTTATGATGCTTTGACTTACTATTTTTTTACCATGATGGTACAAAACAATAGCCATTCAGTAGAAACCATACTTCCAGTATCCATACAATCATTTTATTTTTCACTTTCAGTAGAATATTCAATAAATTACATAAGATATTTAACACTTTATTATAAAACAGGCTTGGTATTAGATGATTTTGCCCAACTGTAGGCAATGTAAGTGTTATGAGTATGTTTAAGGTTGGCTAGGTTAAAACTATGATATTTGTTAGGCTAGCTGTATTAAAAGCATTTTTTATTTAACAATATTTTCAACTTATGCTGGGTTTATCAGGACATAACTCTATTATAAGTCAAGGAGCTTCTGTATTCTACTTTACTTTTTTTTTCTGACTAAGTACATACCTATTTAAGACTATTTAAATATATATATTTTTTCTAAAATTTAAAGTAAACCAACTGTGATAAATTCAGGGACCCTGGTTCTCTTTCAGGTGACCATGGGTAAGTTTCTTTCCTTTGGCCAATAGTTTTAAGCTTTTTATTTATTTTTTTTAACCAAAGTAAGATATGCTGTTTATGTTTTTTGACCAAAGTAAAATTGTTGTAAAAATTCGCAAAATAATGTTACCCTTAGTGTATACATGCACTCATGTTTCTTATGTTCTTCCATTCATTTTCATTAAAATGTAAATTTATAGTGGTCATAATCAGCTAAATTGGTTTTACAACACACTAAGCACATAGTTTATTTTCCTGTAAAAATGAGGATCTTGAACTTCTAGGATCATTTCAAGCTTTAAAATGCTATTATTTAAAGCTTTTATTTTCCTCAGCCTTACAATAATTTACTAATTTTCTTACAAACTCTCTTTTTTTTTAAATTAAG
Seq C2 exon
GTTTGGCGTCTGCTTGATTGGTGTTAGGAGGGAGGATAATAAAAACATTTTGCTGAATCCAGGTCCTCGATACATTATGAATTCTACAGACATATGCTTTTATATTAATATTACCAAAGAAGAGAATTCAGCATTTAAAAACCAAGACCAGCAGAGAAAAAGCAATGTGTCCAGGTCGTTTTATCATGGACCTTCCAGATTACCTGTACATAGCATAATTGCCAGCATGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000162687-KCNT2:NM_198503:15
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.052 A=NA C2=0.128
Domain overlap (PFAM):
C1:
PF0349313=BK_channel_a=FE(47.2=100)
A:
NA
C2:
PF0349313=BK_channel_a=PD(16.1=11.5)
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:
GCCAGCAATCGCCAGAACAAT
R:
TGGAAGGTCCATGATAAAACGACC
Band lengths:
342-1850
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)