MmuALTD0009401-1/2 @ mm10
Alternative 5'ss
Gene
ENSMUSG00000044186 | Nkx2-6
Description
NK2 homeobox 6 [Source:MGI Symbol;Acc:MGI:97351]
Coordinates
chr14:69171948-69175518:+
Coord C1 exon
chr14:69171948-69172048
Coord A exon
NA
Coord C2 exon
chr14:69174632-69175518
Length
0 bp
Sequences
Splice sites
5' ss Seq
CACGTAAGT
5' ss Score
10.16
3' ss Seq
TTCCTTCCATGTGACTTTAGAAA
3' ss Score
6.45
Exon sequences
Seq C1 exon
ATCCGGATGGTTTGAGAGCAGCGACAGGGCACAAGCAGTCCCTTTTCGGTGCACCTGGGAGACAGTCCTGGAGATGGGCTCGAATCCTGTGGGGGAGCCAC
Seq A exon
NA
Seq C2 exon
AAACTCCTCCGGGCACGATCTCCCGACTTGGAGCCAGGAACCCAATGACCGATCGCGGCGTGGGCAACCTGAGTGGCGACATGCGCCGAGGCGGTCCGGTTTCAACCAGAACGCGGCCACAGCGGAAGTCCCGCGTGCTATTCTCCCAGGCCCAAGTGCTGGCCCTGGAGCGGCGCTTCAAGCAGCAGCGATACCTGACTGCGCCCGAGCGTGAGCACTTGGCCAGCGCGCTGCAGCTCACGTCCACGCAGGTCAAGATCTGGTTCCAAAACCGGCGCTACAAGTCCAAGAGTCAGCGCCAGGACCAGACTCTGGAACTGGCCGGCCACCCGTTAGCACCGCGCCGGGTAGCAGTGCCAGTACTGGTACTGGACGGCAAGCCCTGCCTGGATCCCGACGTAGCCGCATTCCTGGGTCCCTACAAAGCCACCTCGCCCTATTCCTGCTTCGGTGGCTACGCGGGCACTCCCTACGACGCTAGCTATGCGAGCCGCTGCACC
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000044186-0-0,1-0-1/2
Average complexity
Alt5
Mappability confidence:
NA
Protein Impact
Protein isoform when splice site is used (Ref)
No structure available
Features
Disorder rate (Iupred):
C1=0.241 A=NA C2=0.435
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0004624=Homeobox=WD(100=27.4)
Main Skipping Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GGAGACAGTCCTGGAGATGGG
R:
CGATCGGTCATTGGGTTCCTG
Band lengths:
99-103
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development
- Ribosome-engaged transcriptomes of neuronal types
- Neural differentiation time course
- Muscular differentiation time course
- Spermatogenesis cell types
- Reprogramming of fibroblasts to iPSCs
- Hematopoietic precursors and cell types