HsaALTD0003043-2/2 @ hg19
Alternative 5'ss
Gene
ENSG00000206503 | HLA-A
Description
major histocompatibility complex, class I, A [Source:HGNC Symbol;Acc:4931]
Coordinates
chr6:29911899-29913058:+
Coord C1 exon
chr6:29911899-29912112
Coord A exon
chr6:29912113-29912174
Coord C2 exon
chr6:29913011-29913058
Length
62 bp
Sequences
Splice sites
5' ss Seq
GGGGTAAGG
5' ss Score
8.05
3' ss Seq
CTGTTTTTGTTCTACCCCAGGCA
3' ss Score
9.83
Exon sequences
Seq C1 exon
ACCCCCCCAAGACACATATGACCCACCACCCCATCTCTGACCATGAGGCCACCCTGAGGTGCTGGGCCCTGGGCTTCTACCCTGCGGAGATCACACTGACCTGGCAGCGGGATGGGGAGGACCAGACCCAGGACACGGAGCTCGTGGAGACCAGGCCTGCAGGGGATGGAACCTTCCAGAAGTGGGCGGCTGTGGTGGTGCCTTCTGGAGAGGA
Seq A exon
GCAGAGATACACCTGCCATGTGCAGCATGAGGGTCTGCCCAAGCCCCTCACCCTGAGATGGG
Seq C2 exon
GCAGTGACAGTGCCCAGGGCTCTGATGTGTCCCTCACAGCTTGTAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000206503-11-20,12-20-2/2
Average complexity
Alt5
Mappability confidence:
NA
Protein Impact
Protein isoform when splice site is used (Ref)
No structure available
Features
Disorder rate (Iupred):
C1=0.349 A=NA C2=0.059
Domain overlap (PFAM):
C1:
PF0765410=C1-set=WD(100=93.5)
A:
NA
C2:
PF066236=MHC_I_C=PD(53.6=88.2)
Main Skipping Isoform:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Rat
(rn6)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GAGGACCAGACCCAGGACAC
R:
GAGGGACACATCAGAGCCCT
Band lengths:
133-195
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)