MmuINT0085525 @ mm9
Intron Retention
Gene
ENSMUSG00000001901 | Kcnh6
Description
potassium voltage-gated channel, subfamily H (eag-related), member 6 [Source:MGI Symbol;Acc:MGI:2684139]
Coordinates
chr11:105885039-105887192:+
Coord C1 exon
chr11:105885039-105885232
Coord A exon
chr11:105885233-105887107
Coord C2 exon
chr11:105887108-105887192
Length
1875 bp
Sequences
Splice sites
5' ss Seq
GACGTGAGT
5' ss Score
9.22
3' ss Seq
TTGCTCTTGTTCCCTACAAGGCA
3' ss Score
5.82
Exon sequences
Seq C1 exon
GGAAGAATGACATCTTTGGGGAGCCTGCCAGTCTCCATGCCAGACCAGGCAAATCAAGCGCCGATGTGCGTGCCCTGACCTACTGCGACCTGCACAAGATCCATCGAGCAGACCTGCTGGAGGTGCTGGACATGTACCCCGCCTTTGCAGATACCTTCTGGAATAAGCTAGAGGTCACCTTCAACCTGCGGGAC
Seq A exon
GTGAGTCTGGGCCTGTGGGGCCGGGGTTGCGATGGTTCACGGAGAGCTGGTTGTGGGTAGCACCCAGGCAGCCTGCTAAGGACTTGTTTTGCCTGGTTGAGGGACTCATCTGACCACTACCTCTTCCCTTCAACTCCTCGTGCATCCTTTGCTGGGATACTTCTGTACCCACTATGCACAAACACACCACTAACTATAGTGATGGCTCCCATTTAATGAGCAGCTACTGCGAGCTAAATCCTGGGCTTCTCTCGGGTTGTTTTAGTCCTGCCCTTGCGTGGGATTTTCTTATCGCCATTATCTAAATGAATAAACTGAGCACCGGAGAGGGTAAGTTAATTGGCCAGAGCCATATGGCTAGTAAAAGGCTGAGCCAAAATGTGGATTCAAATTGTCTGGCCTTAAAACGCAGGCTTTCACATCACAGGGCGCTAAGTTAAAAAGATGGGATCCCAGAGGACTCACGATGCCAGGCATGGGGGTGCAACTGCCTCTTAAGCTTATTACTCAGCAGTCCAGGAGAAATAAAACACCGCTCATTTAAAGAGGCAAAGCCACAAGGGCACGTAAGAGCCAATTTCCGGGGTACTCCAATGTCTTGGGGTTACTATTGCTGTGATAAAACACCATGACCAAAAACAGGTTGGGGAGAGAAGGGTTTATTTCATTACTGCTTGTAGTCCATCATCCAAGAAAGTCAGGGCAGGAACTTAAGGCAGGAACCTAGAATCAGGAGCAGATGCGGAGGCCATGGGGGATGCTACTCGCTCCCTTGTTCACATGACTTGCCCAGCCTGCTTTCATGTAGCACGCAGGACCACCAGCCCAGGGGTGGCACCCCCTGCCATGAGCTGGGTCCTCCCATGTCAATCGGGAAAACATGCCATAGGCTTTCCCTCGGTCCATCTGATGGCGGGGGGCGCTTTTTCTCAGTTGAGTTTCCCTCTTCCCAGATGACGTTAGCTTGTGACAAGTTGAGGTGAAACTAGCTATCACATCAAGTTTGCCAAGGAAGGTGGACATTACTTGTTCAATGGAAGTTCAGAGGTCTTCCTGGAGGAAGAGTCTGAAATCGGCCAGTAAGAAACACAGGGAAACACTGAACCTTGACCCCTGTCCCTCAGCTTCCAGAGAAGTGCTCTCACAGCCTAGGTGGCATACAGCTTCTAGACTGTGGGGCCAAGGTTGGTTGTCCCTCCCCATGCTGTAGCCTCTGTGACTCTCTGTTCCCTTGAACTGCATAAGAGGTCCCCCCCCCACAAAGCACCCTGCTTTGTTGGACTCACTACTGGGAGCCAGCTGGTGGCCTTTGTGTCCAGTGGATGGACACTCGGGTAGAAGGGAGATGGTTTTCATGGTCTTAATTAGCCAGAGTCAACTGTAGCCCCACAGTGCCCTGGAGTCTCATGGTACCAGAAAGGTTGTAGACAAAAATGCTACCATGGGTAGCGCTAGAGTGGACTGAAGATTCCTGACCCAGTGTTCACCAAGAGACACTTCTTACCGACTGTCCCATGCTGGGGTGTGGGCCACTAGGACAATAGAGAAAAGGCAGGCAGGGAGGAGCCCGGCTGCCATCCACCCTCAAGGCTCGCTGCTCTTAAATCTGCCTCCCAAGACTTTCCCGGGGGATTCTACTTGGTTACGTGGGCTAAGGTCATCACCTCCAGGCCTGTTGACCTGCCTGCGAGCCTCTTAGGAAAGAGTCTGCAGGAAGCTTCCAAGTTTCCCTGGGGTGTCTACATGCCTGTTTCTACTTTCTCACTCAGCCGGTGACAAGGGTCACAGAGGGGACCTTGGGGACAGGGAGGAACAAAGAAAGAGACCCTGTCCCAGCCCTGGTCCCTGTCACTTGTTGCTCTTGTTCCCTACAAG
Seq C2 exon
GCAGATGGGGGTCTCCACTCAACACCCCGACAGGCCCCAGGCAACCAAGACCCCCAAGGCTTCTTCCTCAATGACAGCCAATCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000001901-Kcnh6:NM_001037712:9
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.015 A=NA C2=0.793
Domain overlap (PFAM):
C1:
PF0002724=cNMP_binding=PD(53.4=72.3)
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GAAGAATGACATCTTTGGGGAGC
R:
CTGATTGGCTGTCATTGAGGA
Band lengths:
278-2153
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: