MmuALTD1040635-2/2 @ mm10
Alternative 5'ss
Gene
ENSMUSG00000000938 | Hoxa10
Description
homeobox A10 [Source:MGI Symbol;Acc:MGI:96171]
Coordinates
chr6:52231197-52240550:-
Coord C1 exon
chr6:52240450-52240550
Coord A exon
chr6:52240278-52240449
Coord C2 exon
chr6:52231197-52232780
Length
172 bp
Sequences
Splice sites
5' ss Seq
AAGGTAAGT
5' ss Score
11
3' ss Seq
TGTATTCTCTTAAACTCCAGGCA
3' ss Score
7.28
Exon sequences
Seq C1 exon
ACGAGATGGCGCACTCCCGATCAATGTCAAAGCCGCCAGGGAGCCCGGAACCCCAGCGAGATTCTTGGCCTTTGTTCGCTTCTGATACTAAGAGCAGCACG
Seq A exon
GTACGTTATTTCACTTGTCCGGCACCCCTTCGTATTCAAAAAGAGGGGGGGCCCCCGCGCTCAAGAAGTGATTGAGGCTGAAATTTAAAGCAAAGCGCCTTCGTTAGGCCTTTCCGCATCGCGGCGTGGAGAAGCTGCTGCCCCTTGGCAGTGATTTCTGAAATGAGTCAAG
Seq C2 exon
GCAGTTCCAAAGGCGAAAATGCAGCCAACTGGCTCACAGCAAAGAGCGGCCGGAAGAAACGCTGCCCTTACACGAAGCACCAGACGCTGGAGCTGGAGAAGGAGTTTCTATTCAACATGTACCTTACTCGAGAGCGGCGCCTAGAGATCAGCCGTAGCGTCCACCTCACGGACAGACAAGTGAAAATCTGGTTTCAGAATCGCAGGATGAAACTGAAGAAAATGAACCGAGAAAACCGAATCCGGGAGCTCACAGCCAACTTTAATTTTTCCTGATGAAACTTCCAGACAACGTCTTTTCGCTTCCTGAGCGCCTGGACCCATCCTCTGCCTCCAGCCTCTGCCCCAGAACTCACACCTGTGCCGGAGCCCCTTTCTCCCTCCCACACTCGCCATCTCCCAGGCCGTTTCGTCTGTGCAGGGCTGGTTTGTTCTGGCTTTTTTTGTTTGTTTGTTTCTTTGTCTGTTTGCTTGGTGTTTGTTTGCTTGTTTTCTGGGGGA
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000000938-0-4,1-4-2/2
Average complexity
Alt5
Mappability confidence:
NA
Protein Impact
Protein isoform when splice site is used (Ref)
No structure available
Features
Disorder rate (Iupred):
C1=1.000 A=NA C2=0.316
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0004624=Homeobox=WD(100=62.0)
Main Skipping Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
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:
CGCACTCCCGATCAATGTCAA
R:
GGACGCTACGGCTGATCTCTA
Band lengths:
254-426
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- 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