HsaALTA0004092-2/2 @ hg38
Alternative 3'ss
Gene
ENSG00000175879 | HOXD8
Description
homeobox D8 [Source:HGNC Symbol;Acc:HGNC:5139]
Coordinates
chr2:176130796-176131420:+
Coord C1 exon
chr2:176130796-176130943
Coord A exon
chr2:176131317-176131319
Coord C2 exon
chr2:176131320-176131420
Length
3 bp
Sequences
Splice sites
5' ss Seq
AAGGTTGGG
5' ss Score
4.94
3' ss Seq
TTTTTTTTTGTTTTAATCAGCAG
3' ss Score
6.97
Exon sequences
Seq C1 exon
AGACAGCCGATTTTTACGACCCAGCAAGAGGCCGAGCTGGTACAATATCCTGACTGTAAATCGTCCAGTGGTAATATTGGCGAGGACCCAGACCACTTAAATCAGAGCTCGTCTCCTTCTCAAATGTTTCCGTGGATGAGACCACAAG
Seq A exon
CAG
Seq C2 exon
CTCCTGGTAGACGAAGAGGAAGACAAACCTACAGTCGCTTCCAAACTCTAGAGTTGGAAAAGGAATTTCTTTTTAACCCCTATCTGACCAGGAAAAGAAGA
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000175879-3-5,3-4-2/2
Average complexity
Alt3
Mappability confidence:
NA
Protein Impact
Protein isoform when splice site is used (Ref)
No structure available
Features
Disorder rate (Iupred):
C1=0.666 A=NA C2=0.499
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0004624=Homeobox=WD(100=58.2)
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:
GCGAGGACCCAGACCACTTAA
R:
GCGACTGTAGGTTTGTCTTCCT
Band lengths:
107-110
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