HsaALTA0004090-2/2 @ hg38
Alternative 3'ss
Gene
ENSG00000197757 | HOXC6
Description
homeobox C6 [Source:HGNC Symbol;Acc:HGNC:5128]
Coordinates
chr12:54015897-54028921:+
Coord C1 exon
chr12:54015897-54017414
Coord A exon
chr12:54028576-54028695
Coord C2 exon
chr12:54028696-54028921
Length
120 bp
Sequences
Splice sites
5' ss Seq
TCGGTAAGT
5' ss Score
11.78
3' ss Seq
GCCACCTCGCCGGGGGCCAGGAC
3' ss Score
1.08
Exon sequences
Seq C1 exon
AACCATTGCCAGGGAAACCTGCCCTGGGCGCTCCCTTCATTAGCAGTATTTTTTTTAAATTAATCTGATTAATAATTATTTTTCCCCCATTTAATTTTTTTTCCTCCCAGGTGGAGTTGCCGAAGCTGGGGGCAGCTGGGGAGGGTGGGGATGGGAGGGGAGAGACAGAAGTTGAGGGCATCTCTCTCTTCCTTCCCGACCCTCTGGCCCCCAAGGGGCAGGAGGAATGCAGGAGCAGGAGTTGAGCTTGGGAGCTGCAGATGCCTCCGCCCCTCCTCTCTCCCAGGCTCTTCCTCCTGCCCCCTTCTTGCAACTCTCCTTAATTTTGTTTGGCTTTTGGATGATTATAATTATTTTTATTTTTGAATTTATATAAAGTATATGTGTGTGTGTGTGGAGCTGAGACAGGCTCGGCAGCGGCACAGAATGAGGGAAGACGAGAAAGAGAGTGGGAGAGAGAGAGGCAGAGAGGGAGAGAGGGAGAGTGACAGCAGCGCTCG
Seq A exon
GACGTCCTCCCCAACGTCGCCCTCAATTCCACCGCCTATGATCCAGTGAGGCATTTCTCGACCTATGGAGCGGCCGTTGCCCAGAACCGGATCTACTCGACTCCCTTTTATTCGCCACAG
Seq C2 exon
GAGAATGTCGTGTTCAGTTCCAGCCGGGGGCCGTATGACTATGGATCTAATTCCTTTTACCAGGAGAAAGACATGCTCTCAAACTGCAGACAAAACACCTTAGGACATAACACACAGACCTCAATCGCTCAGGATTTTAGTTCTGAGCAGGGCAGGACTGCGCCCCAGGACCAGAAAGCCAGTATCCAGATTTACCCCTGGATGCAGCGAATGAATTCGCACAGTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000197757-2-9,2-8-2/2
Average complexity
Alt3
Mappability confidence:
NA
Protein Impact
5' UTR
No structure available
Features
Disorder rate (Iupred):
C1=NA A=NA C2=0.654
Domain overlap (PFAM):
C1:
NA
A:
NA
C2:
NO
Associated events
Other assemblies
Conservation
Mouse
(mm9)
No conservation detected
Cow
(bosTau6)
No conservation detected
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CTCTCTCCCAGGCTCTTCCTC
R:
GGCTGGAACTGAACACGACAT
Band lengths:
250-370
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- The Cancer Genome Atlas (TCGA)
- Autistic and control brains
- Pre-implantation embryo development