HsaALTA0004087-2/3 @ hg19
Alternative 3'ss
Gene
ENSG00000120093 | HOXB3
Description
homeobox B3 [Source:HGNC Symbol;Acc:5114]
Coordinates
chr17:46629389-46632980:-
Coord C1 exon
chr17:46632893-46632980
Coord A exon
chr17:46629453-46629722
Coord C2 exon
chr17:46629389-46629452
Length
270 bp
Sequences
Splice sites
5' ss Seq
AAGGTAAGC
5' ss Score
10.22
3' ss Seq
CCCCCCAACCCCCATTTCAGGCC
3' ss Score
7.97
Exon sequences
Seq C1 exon
GAGGGGAGATTTGTCGCCTGCCGCTCGCTCTGGGGCTCGATGTGAATATATATTATGTCTGCCTGTTCTCCCCTCGTCGGTGGCTAAG
Seq A exon
GCCGCCACGCACCTGGAGGGCGACTACCAGCGCTCAGCTTGCTCGCTGCAGTCCCTGGGCAACGCTGCCCCACATGCCAAGAGCAAGGAGCTCAACGGCAGCTGCATGAGGCCGGGTCTGGCCCCCGAGCCCCTGTCGGCCCCGCCTGGCTCACCCCCGCCCAGTGCCGCACCTACCAGTGCCACTAGCAACAGCAGTAATGGGGGCGGGCCCAGCAAAAGTGGTCCCCCAAAGTGCGGTCCCGGCACCAACTCCACCCTCACCAAACAG
Seq C2 exon
ATATTCCCCTGGATGAAAGAGTCGAGGCAAACGTCCAAGCTGAAAAACAACTCCCCCGGCACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000120093-10-18,10-17,10-16-2/3
Average complexity
Alt3
Mappability confidence:
NA
Protein Impact
Protein isoform when splice site is used (No Ref, Alt. ATG)
No structure available
Features
Disorder rate (Iupred):
C1=NA A=NA C2=0.937
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Other Skipping Isoforms:
Associated events
Other assemblies
Conservation
Rat
(rn6)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GGGGAGATTTGTCGCCTGC
R:
GTGCCGGGGGAGTTGTTTTTC
Band lengths:
148-418
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
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)