HsaALTA0004091-1/2 @ hg38
Alternative 3'ss
Gene
ENSG00000197757 | HOXC6
Description
homeobox C6 [Source:HGNC Symbol;Acc:HGNC:5128]
Coordinates
chr12:54028696-54029755:+
Coord C1 exon
chr12:54028696-54028921
Coord A exon
NA
Coord C2 exon
chr12:54029655-54029755
Length
0 bp
Sequences
Splice sites
5' ss Seq
GTGGTGAGT
5' ss Score
8.95
3' ss Seq
TTTTGTGCCCGGATCTTTAGGGG
3' ss Score
6.34
Exon sequences
Seq C1 exon
GAGAATGTCGTGTTCAGTTCCAGCCGGGGGCCGTATGACTATGGATCTAATTCCTTTTACCAGGAGAAAGACATGCTCTCAAACTGCAGACAAAACACCTTAGGACATAACACACAGACCTCAATCGCTCAGGATTTTAGTTCTGAGCAGGGCAGGACTGCGCCCCAGGACCAGAAAGCCAGTATCCAGATTTACCCCTGGATGCAGCGAATGAATTCGCACAGTG
Seq A exon
NA
Seq C2 exon
GGGTCGGCTACGGAGCGGACCGGAGGCGCGGCCGCCAGATCTACTCGCGGTACCAGACCCTGGAACTGGAGAAGGAATTTCACTTCAATCGCTACCTAACG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000197757-6-11,6-10-1/2
Average complexity
Alt3
Mappability confidence:
NA
Protein Impact
Protein isoform when splice site is used (Ref)
No structure available
Features
Disorder rate (Iupred):
C1=0.482 A=NA C2=0.415
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0004624=Homeobox=WD(100=55.3)
Other Skipping Isoforms:
NA
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:
CCCTGGATGCAGCGAATGAAT
R:
CCTTCTCCAGTTCCAGGGTCT
Band lengths:
106-130
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Autistic and control brains
- Pre-implantation embryo development