HsaALTD0003046-2/2 @ hg19
Alternative 5'ss
Gene
ENSG00000206503 | HLA-A
Description
major histocompatibility complex, class I, A [Source:HGNC Symbol;Acc:4931]
Coordinates
chr6:29911192-29912174:+
Coord C1 exon
chr6:29911192-29911261
Coord A exon
chr6:29911262-29911320
Coord C2 exon
chr6:29911899-29912174
Length
59 bp
Sequences
Splice sites
5' ss Seq
CGGGTACCA
5' ss Score
3.25
3' ss Seq
TTTCTGACTCTTCCCGTCAGACC
3' ss Score
7.9
Exon sequences
Seq C1 exon
CTCAGATCACCAAGCGCAAGTGGGAGGCGGCCCATGAGGCGGAGCAGTTGAGAGCCTACCTGGATGGCAC
Seq A exon
GTGCGTGGAGTGGCTCCGCAGATACCTGGAGAACGGGAAGGAGACGCTGCAGCGCACGG
Seq C2 exon
ACCCCCCCAAGACACATATGACCCACCACCCCATCTCTGACCATGAGGCCACCCTGAGGTGCTGGGCCCTGGGCTTCTACCCTGCGGAGATCACACTGACCTGGCAGCGGGATGGGGAGGACCAGACCCAGGACACGGAGCTCGTGGAGACCAGGCCTGCAGGGGATGGAACCTTCCAGAAGTGGGCGGCTGTGGTGGTGCCTTCTGGAGAGGAGCAGAGATACACCTGCCATGTGCAGCATGAGGGTCTGCCCAAGCCCCTCACCCTGAGATGGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000206503-8-15,9-15-2/2
Average complexity
Alt5
Mappability confidence:
NA
Protein Impact
Protein isoform when splice site is used (Ref)
No structure available
Features
Disorder rate (Iupred):
C1=0.094 A=NA C2=0.349
Domain overlap (PFAM):
C1:
PF0012913=MHC_I=PD(49.2=94.6)
A:
NA
C2:
PF0765410=C1-set=WD(100=93.5)
Main Skipping Isoform:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Rat
(rn6)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GGAGCAGTTGAGAGCCTACCT
R:
CTGCCAGGTCAGTGTGATCTC
Band lengths:
137-196
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)