HsaEX0030378 @ hg19
Exon Skipping
Gene
ENSG00000198353 | HOXC4
Description
homeobox C4 [Source:HGNC Symbol;Acc:5126]
Coordinates
chr12:54447701-54449111:+
Coord C1 exon
chr12:54447701-54448145
Coord A exon
chr12:54448262-54448310
Coord C2 exon
chr12:54448634-54449111
Length
49 bp
Sequences
Splice sites
3' ss Seq
CCTTCCCCCTCTCTCTCCAGGAG
3' ss Score
13.7
5' ss Seq
TGGGTAATT
5' ss Score
6.19
Exon sequences
Seq C1 exon
AAATTAATGATCATGAGCTCGTATTTGATGGACTCTAACTACATCGATCCGAAATTTCCTCCATGCGAAGAATATTCGCAAAATAGCTACATCCCTGAACACAGTCCGGAATATTACGGCCGGACCAGGGAATCGGGATTCCAGCATCACCACCAGGAGCTGTACCCACCACCGCCTCCGCGCCCTAGCTACCCTGAGCGCCAGTATAGCTGCACCAGTCTCCAGGGGCCCGGCAATTCGCGAGGCCACGGGCCGGCCCAGGCGGGCCACCACCACCCCGAGAAATCACAGTCGCTCTGCGAGCCGGCGCCTCTCTCAGGCGCCTCCGCCTCCCCGTCCCCAGCCCCGCCAGCCTGCAGCCAGCCAGCCCCCGACCATCCCTCCAGCGCCGCCAGCAAGCAACCCATAGTCTACCCATGGATGAAAAAAATTCACGTTAGCACGG
Seq A exon
GAGCGACTCTGGGTTAGCACAATTGAACTGGATTTACGAGCGAGAATGG
Seq C2 exon
TGAACCCCAATTATAACGGAGGGGAACCCAAGCGCTCGAGGACAGCCTATACCCGGCAGCAAGTCCTGGAATTAGAGAAAGAGTTTCATTACAACCGCTACCTGACCCGAAGGAGAAGGATCGAGATCGCCCACTCGCTGTGCCTCTCTGAGAGGCAGATCAAAATCTGGTTCCAAAACCGTCGCATGAAATGGAAGAAGGACCACCGACTCCCCAACACCAAAGTCAGGTCAGCACCCCCGGCCGGCGCTGCGCCCAGCACCCTTTCGGCAGCTACCCCGGGTACTTCTGAAGACCACTCCCAGAGCGCCACGCCGCCGGAGCAGCAACGGGCAGAGGACATTACCAGGTTATAAAACATAACTCACACCCCTGCCCCCACCCCATGCCCCCACCCTCCCCTCACACACAAATTGACTCTTATTTATAGAATTTAATATATATATATATATATATATATATAGGTTCTTTTCTCTCT
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000198353_CASSETTE2
Average complexity
S
Mappability confidence:
100%=100=100%
Protein Impact
ORF disruption upon sequence inclusion (Alt. Stop)
No structure available
Features
Disorder rate (Iupred):
C1=0.792 A=1.000 C2=0.669
Domain overlap (PFAM):
C1:
NO
A:
NO
C2:
PF0004624=Homeobox=WD(100=47.9)
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GCCAGCAAGCAACCCATAGTC
R:
CTCTAATTCCAGGACTTGCTGCC
Band lengths:
132-181
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- The Cancer Genome Atlas (TCGA)
- Genotype-Tissue Expression Project (GTEx)
- 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)