MmuINT0085495 @ mm9
Intron Retention
Gene
ENSMUSG00000035355 | Kcnh4
Description
potassium voltage-gated channel, subfamily H (eag-related), member 4 [Source:MGI Symbol;Acc:MGI:2156184]
Coordinates
chr11:100601692-100603312:-
Coord C1 exon
chr11:100602607-100603312
Coord A exon
chr11:100601936-100602606
Coord C2 exon
chr11:100601692-100601935
Length
671 bp
Sequences
Splice sites
5' ss Seq
GAGGTAGGT
5' ss Score
9.65
3' ss Seq
CTGTTTCTGTCTCTCTACAGGCT
3' ss Score
13.55
Exon sequences
Seq C1 exon
ATCTCCCGTCTCAATCAGGAAGTGTCTCAGCTGAGCCGGGAGCTGCGGCAAGTGATGGGTCTCTTACAGGCCAGGCTGGGACCCCCAAGTCACACAGCTGGTCCAGCTTGGCTCCCAGACCTTCCTTGCCCCCACCAGAGACTACCATGCATCTCTCCTCATATGTCTGGACCACCACCTGGTCTCCAGAATACTACACTCGCTGTAGTCCACTGTCCAGCCAGTGTTGGGACAGTGGAGATAGGGGCCACCCCCTCAGAGCTGAGACCTTCCACGATACCACCCTATCCCTCGGAACCTGATCCTCTGGGACCCTCTCCAGCGCCAGAGGCTCCTCCCCTGACCCCAAGCCTCCTGAAGCACAGCTTCCAGTCTGGGTCAGACACATTCCACTGACCCTGGCCTTGGGCCTAGGCCTGTCTGGGGTAGGCTTTACCACCTGCCATCCAGGGAGGCGCTGGGCTCCTTGGCCTCTTGCCTTGGGGTCAGCAGCTGCCAGCTGGACTGGTTGGCTCTGGATTCTCTGGACTTTTTAAACAACGAATGGCCACATCTAACCCCGTTCCATTTTCTAAACCATCCCCCATCCTCCTCTTCTGGGAGGGGAGTCACTTGAAGCCATGGAATCCAGCAGGCATGAAATGGACCATGGCGCCCTGTTGGGCTACGCAGAGGAGATGTCTTACTTTCTCCCGAAGACTTGGAG
Seq A exon
GTAGGTATGGACTGGGAACAGAAGAATGGTCAAGAGCAAAGGTCTAACCTAGTAAAGGAAGGCTTGAGGTTAGACCAGGCAGGGTCTAGAGTGAGAGGGCTAGATGACATTATAGTACTATGGAGCTCTTCTGTCCCAGATTCTGAGTCCTTTGCAGAGGATCCTGAGAATAATGTCACCTTGAGGAGAGTGAGTTTGAGATTCTAGCCATCATTTGAGAAGCCCAGGACATCTTAGGCCTCCTGCCAGCAGCCAAGCTGAAGGAGTTCACTTCACCCCATGGCACACACAAAAAACAACTGAGAGCTCCAGATGTGTCTTTGGCTCTCAGAACACTTCTTTTCTTCTTCAAACTCTGAGTTAGTTACCAGCATCGAACTCCAGATAGAACCACAAAATATTCAGTATTCTAACTTCTCAAGAAAAAAAAAAAAAAAGACAACAATGTCTGGCTATCAAGAGCCAACATTCATCTGAAATAGTCCCCATTTCTTCAGTCTCCTGCTTGTTGATCATTTCTTAATGTCCAATTGGCTTGCCTTATTTGTTTGGTCCCTCTGTTTTCTTCAGTTTGCAATCCCTGTCTTAGAGTGGGCGCCAAGGGGGTCCTAATAATGTCTGTTCGTACTCTTGACTTGGGCCTGTCAACATCTGTTTCTGTCTCTCTACAG
Seq C2 exon
GCTGTCATGCAAGGTGGTTCCTTCTGCTGTCAGCAGCTCAAAGCATTCTAGCATTACCCTTCTGCAGGTCCCACCTCCCAACATCAGCCAAACCTGCATCCCCTCCCTCCCAACATGGTCTCAACCTCAGGGAGGGTCTGGGCAACTCCCAAGCCCTCTCTGGTTTCCAGCCCTCCTTTCTCACTCAATGCCCCACCCAGGCGCACTTTTGGATAAAAAAAAAATAAATCCATATATTTTTGTA
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000035355-Kcnh4:NM_001081194:16
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
3' UTR
No structure available
Features
Disorder rate (Iupred):
C1=0.885 A=NA C2=NA
Domain overlap (PFAM):
C1:
PF0148612=K-box=PD(53.5=17.4)
A:
NA
C2:
NA
Main Skipping Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Rat
(rn6)
No conservation detected
Chicken
(galGal4)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GAATGGCCACATCTAACCCCG
R:
GAGTGAGAAAGGAGGGCTGGA
Band lengths:
351-1022
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: