HsaALTA0004091-2/2 @ hg19
Alternative 3'ss
Gene
ENSG00000197757 | HOXC6
Description
homeobox C6 [Source:HGNC Symbol;Acc:5128]
Coordinates
chr12:54422480-54423539:+
Coord C1 exon
chr12:54422480-54422705
Coord A exon
chr12:54423415-54423438
Coord C2 exon
chr12:54423439-54423539
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
ENSG00000197757-3-7,3-6-2/2
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=0.497 A=NA C2=0.417
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0004624=Homeobox=WD(100=55.3)
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Rat
(rn6)
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
Other AS DBs:
FasterDB (Includes CLIP-seq data)
AS-ALPS (AS-induced ALteration of Protein Structure, links to PINs)
APPRIS (Selection of principal isoform)
DEU primates (Only for human)