MmuALTD1000685-1/3 @ mm10
Alternative 5'ss
Gene
ENSMUSG00000001656 | Hoxc11
Description
homeobox C11 [Source:MGI Symbol;Acc:MGI:96193]
Coordinates
chr15:102955107-102957708:+
Coord C1 exon
chr15:102955107-102955207
Coord A exon
NA
Coord C2 exon
chr15:102956469-102957708
Length
0 bp
Sequences
Splice sites
5' ss Seq
CCAGTAGGT
5' ss Score
5.41
3' ss Seq
TGCCCTTCCCCTCCCTCCAGACG
3' ss Score
12.3
Exon sequences
Seq C1 exon
GGCCGGTGCTGAGGCCGAGGCCGAGGAGGAGAACACGAATCCCAGCTCGTCCGGTTCTTCCCACTCGGCGACCAAGGAGCCGGCCAAGGGAGCCGCCCCCA
Seq A exon
NA
Seq C2 exon
ACGCCCCCCGCACCCGCAAGAAGCGCTGCCCTTATTCGAAATTCCAGATCCGGGAACTGGAGCGAGAGTTTTTCTTCAACGTGTACATCAACAAAGAGAAGCGGCTGCAGCTGTCCCGGATGCTGAACCTGACAGACCGACAAGTGAAAATTTGGTTTCAGAACAGGAGAATGAAAGAAAAAAAACTGAGCAGAGACCGGCTGCAGTATTTTTCAGGAAATCCACTGCTGTAACTGCAGACCTGACCCTTTGGGGTGGGAGGGAGGGAAAGAGGGAAATTTATTTTATTTTATTTTATTTTTTATTTTCTAACTCGTCTTTTTTTTTTCCGCGGGTGGAAAACTGGACTGTGGCCAGGGCTGGCCCCCCAATGCCGTTACTGGCACTTCCTTCTAGAACCTCCTTGGCCTTGGGTCTAATTCACTGTAGGGAACAGAGACCCAGCCTGGAAAAGGAGGTGAGGGAAGTGTCTGACCCGTGGTTAGTGGACCCCGTGGCGC
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000001656-1-0,2-0,3-0-1/3
Average complexity
Alt5
Mappability confidence:
NA
Protein Impact
Protein isoform when splice site is used (Ref)
No structure available
Features
Disorder rate (Iupred):
C1=0.399 A=NA C2=0.195
Domain overlap (PFAM):
C1:
PF120453=DUF3528=WD(100=62.7)
A:
NA
C2:
PF0004624=Homeobox=WD(100=73.1)
Main Skipping Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GAACACGAATCCCAGCTCGTC
R:
AATAAGGGCAGCGCTTCTTGC
Band lengths:
107-111
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