MmuINT0085816 @ mm9
Intron Retention
Gene
ENSMUSG00000058740 | Kcnt1
Description
potassium channel, subfamily T, member 1 [Source:MGI Symbol;Acc:MGI:1924627]
Coordinates
chr2:25756729-25757510:+
Coord C1 exon
chr2:25756729-25756878
Coord A exon
chr2:25756879-25757271
Coord C2 exon
chr2:25757272-25757510
Length
393 bp
Sequences
Splice sites
5' ss Seq
GAAGTACGT
5' ss Score
7.46
3' ss Seq
TCCAGGCCATGTCTGCTCAGATA
3' ss Score
4.13
Exon sequences
Seq C1 exon
GGAAGGACAGGAGTCTCCCGAGCAGTGGCAGCGCACGTACGGGAGGTGCTCGGGCAACGAGGTGTACCACATTCGCATGGGTGACAGTAAATTCTTCCGGGAGTATGAGGGCAAGAGCTTCACCTACGCAGCCTTCCACGCGCACAAGAA
Seq A exon
GTACGTGGGGCTCGGGGTGGCCTAGAGGGTTGGAGCCCGCTATGCCCACCACCACTGGGCTACTCGTCCTCCACCCAGGGCCAGGTCATTATGAGTGGGGGTCCTGGGCAGGAGATCACAGAGTCTCAGCTAAGGGCAGTGTAACCCGGCTCTGCGCACCTTGTGAGGTGGTCAGGACATCCCAGGGCAAGGTTCATGTAAGAACCTGCCGCAAAGCCTCTCCTTTCTGAAGCTTCTAATGCTGACCTGGGATCCTCAAGTCCCTAACGCCTGAGGGGAGGGCTTGTCCAAGAAGTCCAGGCGTGGTCCCTGGGAGGAGACTAAGTAGCTCAGGACAATGTGAGCCACAGGCTGCCAGGAGTGGCACTGAAGGTCCAGGCCATGTCTGCTCAG
Seq C2 exon
ATATGGGGTGTGCCTCATCGGGCTGAAGCGTGAGGAGAACAAGAGTATCCTGCTGAACCCAGGACCACGGCACATCCTGGCTGCCTCCGACACCTGCTTCTATATCAATATTACCAAGGAGGAGAACTCAGCTTTCATCTTCAAACAGGAGGAGAAGCAGAAGAGACGGGGCCTTGCAGGGCAGGCACTATATGAAGGGCCCTCCCGGCTCCCAGTGCATAGCATCATCGCCTCTATGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000058740-Kcnt1:NM_001145403:17
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.196 A=NA C2=0.085
Domain overlap (PFAM):
C1:
PF0349313=BK_channel_a=FE(47.2=100)
A:
NA
C2:
PF0349313=BK_channel_a=PD(8.5=11.1)
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:
GAAGGACAGGAGTCTCCCGAG
R:
GCCCTTCATATAGTGCCTGCC
Band lengths:
349-742
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development
- Muscular differentiation time course
- Spermatogenesis cell types
- Reprogramming of fibroblasts to iPSCs
- Hematopoietic precursors and cell types
Other AS DBs: