HsaINT0084751 @ hg19
Intron Retention
Gene
ENSG00000162687 | KCNT2
Description
potassium channel, subfamily T, member 2 [Source:HGNC Symbol;Acc:18866]
Coordinates
chr1:196397235-196398887:-
Coord C1 exon
chr1:196398707-196398887
Coord A exon
chr1:196397400-196398706
Coord C2 exon
chr1:196397235-196397399
Length
1307 bp
Sequences
Splice sites
5' ss Seq
CAGGTAAAC
5' ss Score
7.82
3' ss Seq
ATGTGGAAAATATATTACAGTTT
3' ss Score
2.48
Exon sequences
Seq C1 exon
CATTTGTGGGATCCAACATCTGGAACGAATAGGAAAGAAGCTGAATCTCTTTGACTCCCTTTATTTCTGCATTGTGACGTTTTCTACTGTGGGCTTCGGGGATGTCACTCCTGAAACATGGTCCTCCAAGCTTTTTGTAGTTGCTATGATTTGTGTTGCTCTTGTGGTTCTACCCATACAG
Seq A exon
GTAAACAAAACCATCTTATATTGCATAGAAATGTACAGAGACATGAAATTGAATCCTCCACATTTAATAAGAAATGGAAAGTGGCTTATTTATCTAACACTAATTTACTAACACATACTATCATTACATTTAATCAATTACATAAATTACTGCAGAAATGTCATTTTACATTTTATTAGAAACACCGAGTTGCTTTTTTTTCCTTCCAGTCATGACTGACAGCACTCATCTTATTTCAATCATTCAAGATTTTTTTTAGTATAGGGTACTTAATTATATTAAATATAGAATAACATAGTTTTTAATTATAGGATGATAGATCAAAGAAATAAATTTGTGAAGGGTTGATTTCTCTTGGTTCTTCAAAATAAACCACAAAGTCATACACTGCAATGAAGAAAAATCTATTACTTATGTTTGTCAAATAAAATCTGGGCCAGGTGCAGGGCTCATGCCTATAATACCAGTATTTTGGGAGGCTGAGGCAGGTGGATGGCTTGAGCCAAGGAGTTGAAGATGAGCTTGGGCTATAAGGTAAAACCCCATCTCTACAAAAAAAAAAAAAAAAGTCTGAACATGGTATGTAAATATTATGTGGCACTTTGGGGAGTGAGTAGGGAGGTTGCAAAGGGATGGATATATAAATGGAATTAAAGATAAGTAGATGCAATCTCTAACTCTTTCCTATAATAAGCCCTGGCTGCCCATGTGTGGGCAGATCAGAAGCAGGCTATAGGGAAATGCAAATCAAACTTGCATATTCCATTGCAAAACTTTGGCCGCAATGTATCTGAATAGAATACCTGCAAAAATGGCCTTCCTGCTCCGATAAATTCATGCATGTCTTTCTTCCTGACATACCCTCCCTTGCACCTTTCACTTTCCTCCGTTAATGGCTACTGTACAGCTAGAATGTGGCCTTGTGTGTTATGGTAAGAGTAACTCCTATTGCATGAGATATGGTTAGAATTTGACAGAGAATGTGGGAAAATAGCAATGAGGCTTTTCTCTTTCACTCAGCTCTACTGGACATAAAGCAGAGGTACAAACCTCTTAGTGGCCTGTTATTATGTGATAGCAAAATCATGTTAATATGTTTCCTTAGAGACCCGAAGCCCCTGGGAGACATTTGCAGCCTCTGTAGAAATTATATGAAAAGTCTGTCGTTGAAGGGGAATACTGACAATTAGAATCTCAATGAGTTCCATCTAGGAAATTGAAAATACCTAATAAACAATAGATGTATTGCATTGATTTATTTATTTCCTTACTGTGTTTTTCATTCACATGTGGAAAATATATTACAG
Seq C2 exon
TTTGAACAGCTGGCTTATTTGTGGATGGAGAGACAAAAGTCAGGAGGAAACTATAGTCGACATAGAGCTCAAACTGAAAAGCATGTCGTCCTGTGTGTCAGCTCACTGAAGATTGATTTACTTATGGATTTTTTAAATGAATTCTATGCTCATCCTAGGCTCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000162687-KCNT2:NM_198503:9
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=FE(71.4=100)
A:
NA
C2:
PF0788511=Ion_trans_2=PD(9.5=14.5)
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:
CATTTGTGGGATCCAACATCTG
R:
TGGAGCCTAGGATGAGCATAGA
Band lengths:
345-1652
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)