MmuINT0085488 @ mm9
Intron Retention
Gene
ENSMUSG00000035355 | Kcnh4
Description
potassium voltage-gated channel, subfamily H (eag-related), member 4 [Source:MGI Symbol;Acc:MGI:2156184]
Coordinates
chr11:100618881-100621092:-
Coord C1 exon
chr11:100620844-100621092
Coord A exon
chr11:100619115-100620843
Coord C2 exon
chr11:100618881-100619114
Length
1729 bp
Sequences
Splice sites
5' ss Seq
CGCGTGAGT
5' ss Score
8.4
3' ss Seq
TTGACTTCTCCCTCCTGTAGACA
3' ss Score
10.32
Exon sequences
Seq C1 exon
TGCGGAGCAGAGCTTAGAACTAACAGGTTCAGAGCACACAGGCAGCGGCGGCGAGAGGAGGGGAGGAGGCAGGCCGGCGCATGGGGCGCCCCGGCCCCGCCGGTAGCGCGCCCCCTCCGGCCAGGCCGCGCTGAACGCAGCCCGCGCAACGCCTCGAATCCGTACCCGGGGCCATGCCGGTCATGAAGGGGTTGCTGGCCCCGCAAAACACCTTTCTGGACACCATCGCCACCCGCTTTGACGGCACGC
Seq A exon
GTGAGTTGGGCCGGCTGGGTCAAGTCTCCTTGGGACAGGGTGGGTATCTGGATGTGGTGAGATCAGAGGAGAGAGAATGGAGTGCTGGATCTCCTAAAACCGTGGCAAAGAAACGGGGTGCAGAACCCTTGAGAGTGGAGATCAAGACATGAAGCGCCGAGGGTGGAGGGGAAGGTTAGGGGGTGTGACTCAAGGCAAAAGCGGCTCTTTGTGCCACAAGACGGAGGAGGGGCCTTGGGAGCCACCCACACCAGGGCAGAGCTGAGCTGGGAGTGTGTATAGAGGTATCTGTGGTGTGGAGATGGGACAAAGTGCTCTGGTGACTGCAGCTGCCTCTGCCCCAGAAAAGAGAGAGAACAGACTTCGGCAAGACCTAACCGCATTAAGGTCACGCGCCCCCAAATCATGAGATATCTTTGTGTGAGGTGGGCGAGGCAAAGCGGGGGCAAGTACTTGAGAACGAGAAAACTCCCTGCTAGCCCACCTGAGCTGGGTTCCGAAGTTCAGCACCCTGGACAGCCGCACAGCTCCTTCCCCGCCTCTTCTCCCGCCATTCCCAACTCTGGAACCCCTAGGTCTTCCTTTGTCCCTTTTCGAAACCCTGGCCGGCATTAGGAGGGTGGGGGAGCGGTAGCCGAGGGCGGAAACCGAGCCTCCAGGGCCCTACCCCCCCCCCCAACCTCTCTTGTTTCCATAGCGCCAATCACCGAGGCAACGGGCCCTGGGATGGAAGAAGTAGGCTGTGCCCAGGACCCAGTGCTTCCTAGGAACCCTCAGTGTCCCGATCAGACACCCCATCCCCTGACAGTACCCTCTCCTAGGGTCCTTGGACTGTTTGTGCCTCCTACCTCATCAACTAAACCTATCTCTGCGTGTCCCTCCACCCCCAAACCTCTAATCCACTGAAACTAGAGGGAGCCAACTCAGGTTCTGGTGCTGGGGTGGCTGCAGCTCACACCTCAATGTCTTCTCCAGTTTGACTTTGCGCATAAGGAACAGATCCTTTGAAACTCCTTAAAAAAAAAATATATATATATATATATATATATATATCAAAAAGTCGGCATTTCCTGGAAGGCAAGAAAGAGGGATGTGTCTTCCACAGTCTTTCCCTTACTTTAAGCACATTTATGAGTTTGGAAATTTTTCTGCCTTTTGGTTTAACAATAAGAGAGTGTGACATCATCAGAATCTTTGTCCTTGCTCATTAAAAGAGGATGCTGGGGTAGTATCCAAGGATGTGCTTCCAAAATTGAGTGAATTGGGAGTGGGGGAGAATCTTCTAAGTGCCAGCAGGCCCTCCTTCCCAAGTTACCTGATACACCCCATATCCAGGAGGGAAAGGCACATTGTGTCCCACTTTGCAGATAAGAAAGCTGAGGCCTTAAGCCACATTATGTATGGCCACATTATGAGGTGGTAGAAGTGAGTGCTGGAGTCCCTGCCCTTTCCATTCTTAGTTGCTTTCTGCAGTCACACTTCTCCAGCTTGAAGGTAGGAGCATGAACCACACGGCCTCATTGGGGTTCCTTCTCTAGCCCTTCATGGACTCCGGGCCACCCTTGTTGTGTGCCTTCTGCTCATTTCAGAACATCTCAGAGGGAGATTAGGTACCACCCGGAAGCTTCTAGCTCTCTGGTCTCTGTCCATGACTTGAGGGAACTGTTGTTCATGTCGAGGTTAGCTCCCTTCTTGGCTTGGCCCTGACCTTGACTTCTCCCTCCTGTAG
Seq C2 exon
ACAGCAACTTCCTTCTGGCCAATGCACAGGGCCCACGGGGTTTTCCCATCGTCTACTGCTCTGACGGCTTCTGTGAGCTCACAGGCTACGGCCGCACCGAGGTCATGCAGAAAACCTGTAGCTGTCGGTTCCTCTATGGCCCAGAGACCAGTGAACCAGCCCTGCAACGGTTGCAAAAAGCCCTGGAGGGCCACCAAGAACACCGAACTGAAATCTGCTTTTACCGAAAGGATG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000035355-Kcnh4:NM_001081194:1
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.089
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF134261=PAS_9=PU(70.6=97.5)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Rat
(rn6)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AACAGGTTCAGAGCACACAGG
R:
GGTTTTCTGCATGACCTCGGT
Band lengths:
344-2073
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: