HsaALTA0004091-2/2 @ 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
chr12:54029631-54029654
Coord C2 exon
chr12:54029655-54029755
Length
24 bp
Sequences
Splice sites
5' ss Seq
GTGGTGAGT
5' ss Score
8.95
3' ss Seq
GCTTTGCTGATTGCTTTTAGTGT
3' ss Score
5.96
Exon sequences
Seq C1 exon
GAGAATGTCGTGTTCAGTTCCAGCCGGGGGCCGTATGACTATGGATCTAATTCCTTTTACCAGGAGAAAGACATGCTCTCAAACTGCAGACAAAACACCTTAGGACATAACACACAGACCTCAATCGCTCAGGATTTTAGTTCTGAGCAGGGCAGGACTGCGCCCCAGGACCAGAAAGCCAGTATCCAGATTTACCCCTGGATGCAGCGAATGAATTCGCACAGTG
Seq A exon
TGTGTTTTGTGCCCGGATCTTTAG
Seq C2 exon
GGGTCGGCTACGGAGCGGACCGGAGGCGCGGCCGCCAGATCTACTCGCGGTACCAGACCCTGGAACTGGAGAAGGAATTTCACTTCAATCGCTACCTAACG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000197757-6-11,6-10-2/2
Average complexity
Alt3
Mappability confidence:
NA
Protein Impact
Protein isoform when splice site is used (No 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 Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Mouse
(mm9)
No conservation detected
Cow
(bosTau6)
No conservation detected
Chicken
(galGal4)
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
- The Cancer Genome Atlas (TCGA)
- Autistic and control brains
- Pre-implantation embryo development