MmuINT0085846 @ mm9
Intron Retention
Gene
ENSMUSG00000052726 | Kcnt2
Description
potassium channel, subfamily T, member 2 [Source:MGI Symbol;Acc:MGI:3036273]
Coordinates
chr1:142404277-142406190:+
Coord C1 exon
chr1:142404277-142404426
Coord A exon
chr1:142404427-142405960
Coord C2 exon
chr1:142405961-142406190
Length
1534 bp
Sequences
Splice sites
5' ss Seq
AAAGTATGT
5' ss Score
6.93
3' ss Seq
TATTCTTCTTTTAAATTAAGGTT
3' ss Score
6.68
Exon sequences
Seq C1 exon
AGAAGGGCAGCAGTCACCTGAACAGTGGCAGAAGACTTACGGGAGGTGCTCAGGAAACGAAGTCTATCACATCGTTTTGGAAGAAAGTACATTTTTTGCTGAATATGAAGGGAAGAGTTTTACCTATGCTTCTTTTCATGCCCACAAAAA
Seq A exon
GTATGTTTCTGTTTCCAGTGAAGAATTCACTCATCAACCAACCAATCAGAACAGTTAAACTGCTTTCCAAATTAGCGCTCATACGTTTAGACTTTTTAAGCATAATTTTTGTCCTATTATAAACTATAGTCTTTGTCATTTCTGTAAGTTATTTAAACCAGGAGGAAAATACATTAGGAAATCTACTCTACCATATCTTAGATACTCACATCACCTATCCTAAGAATTTATAGCCATTCAATAATGTGCTTGTTTCATAAATTAAATTTAAAGTGATATTTAGTTTTATTTATGTTTAAAATAACAGAAACACTTGAAAAATAGTTCAACAAAAGAGGGAAGAGAAAAAAAAACATTTCCCCGTTTGGTCTTTTGAATCATAATCACATGTAACTCAGGGTGTCCTCAAACTCCCTATGTGGACAAGGCTAATCTTGCTGACTTTCCACTTCATTTCTAAAACAACACATAACTCTCCAAAAAATAGAGAAATGGACATTAGACACTTTACTTTCCCTTTTGTACTAAATTGATAACTTAAGGAATTAAAAATATATCAAAATTCAGCTATACTAAAGTATATTAATGAAACCTATATGGATGCCTTATGTTAATATATTCTATTTAATATATAATGTACTCAAATTTAACACTCTATGATAATAACATTTATACGTATTTTACTACTACATATATTTTGAAACTTGACTTATTCTGTTTTGTATTAAGATGAATTTTGAAAGTTAGAACATTACCAAAGATCTGTAATAAATATTTTGATACACTATTACACTCAAAGTTTTAAAGTTCTCCTATTGATCATGTATGATCATTGAGGAACATTTGAAATGTTTCTTTCTTGAATACATGAAAGGCGGTAGAAGTGGTAAGCAAGGCAATTCAGAGACATCACTCTTTTCACATGACATTTCATAAGAGTCTCCCTTTTGCCAATCACTTGTAAATATTTTAAGCAAGGTAAGACATATTGTTCATAGCTTTGATATCATTAGTTATCTTAAGAATTATAAAGCAATGTTACATCTACTTATGACAAGCTAATCTTGTATATTGTTTTTATTTAGTTATTTAATTTTACATTTATTTACATTTCAAGTGTTACCCCCTTACATGGTTCCCCCCTCATGTAAACCTCCTATTCCATTCCTCCTTCCCCTGCTTCTATGAGGGTGTTCTTCCACCCACCTGCCCACTTCCCGCTCCCTGCCCTTGATTTCCTTACACTGGGGCATCTATCAAGCCTTTATAGAACCTATATTGTTTTATTTTTTTCATTTATATATATCATAATGCTTAAAACCAATTGAATTTATTCTTTTTCCTTTCAAAGTGAGATTATTAAATGTTAGGACCCTCTTGGGCTCCCTAGTTCTATTATTTGATGTTCTTATTTTGTTCTGTTTAATTAGAGTTGGCTAATTTTCTTACAAATATTAGCTTTTAAAAGAACAAAAAGCTAAGGACTTTTCCAAGTTGTAATTCTTAAACTCTTATATTCTTCTTTTAAATTAAG
Seq C2 exon
GTTTGGTGTCTGCTTGGTTGGTGTTAGGAGGGAGGATAATAAAAACATTTTGCTGAATCCAGGTCCTCGATACATTATGAATGCTTCAGACATATGTTTTTATATTAATATTACCAAAGAAGAAAATTCAGCATTTAAGAATCAAGACCAACAGAGAAAAAGTAATGTGTCAAGGTCATTTTATCATGGGCCTTCCAGATTGCCTGTCCACAGCATCATTGCCAGCATGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000052726-Kcnt2:NM_001081027:15
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.078 A=NA C2=0.126
Domain overlap (PFAM):
C1:
PF0349313=BK_channel_a=FE(47.2=100)
A:
NA
C2:
PF0349313=BK_channel_a=PD(14.5=10.3)
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:
CAGTCACCTGAACAGTGGCAG
R:
TGATGCTGTGGACAGGCAATC
Band lengths:
358-1892
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: