HsaALTA0004030-2/2 @ hg19
Alternative 3'ss
Gene
ENSG00000204642 | HLA-F
Description
major histocompatibility complex, class I, F [Source:HGNC Symbol;Acc:4963]
Coordinates
chr6:29691435-29692008:+
Coord C1 exon
chr6:29691435-29691704
Coord A exon
chr6:29691950-29691966
Coord C2 exon
chr6:29691967-29692008
Length
17 bp
Sequences
Splice sites
5' ss Seq
CTGGTGAGT
5' ss Score
10.1
3' ss Seq
TGACTGCGGGGACCGGCTAGGGT
3' ss Score
-0.4
Exon sequences
Seq C1 exon
GCTCCCACTCCTTGAGGTATTTCAGCACCGCTGTGTCGCGGCCCGGCCGCGGGGAGCCCCGCTACATCGCCGTGGAGTACGTAGACGACACGCAATTCCTGCGGTTCGACAGCGACGCCGCGATTCCGAGGATGGAGCCGCGGGAGCCGTGGGTGGAGCAAGAGGGGCCGCAGTATTGGGAGTGGACCACAGGGTACGCCAAGGCCAACGCACAGACTGACCGAGTGGCCCTGAGGAACCTGCTCCGCCGCTACAACCAGAGCGAGGCTG
Seq A exon
GGTCTCACACCCTCCAG
Seq C2 exon
GGAATGAATGGCTGCGACATGGGGCCCGACGGACGCCTCCTC
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000204642-4-18,4-17-2/2
Average complexity
Alt3
Mappability confidence:
NA
Protein Impact
Protein isoform when splice site is used (Ref)
No structure available
Features
Disorder rate (Iupred):
C1=0.055 A=NA C2=0.150
Domain overlap (PFAM):
C1:
PF0012913=MHC_I=PU(50.3=98.9)
A:
NA
C2:
PF0012913=MHC_I=WD(100=95.3)
Other Skipping Isoforms:
NA
Associated events
Conservation
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TATTGGGAGTGGACCACAGGG
R:
CATGTCGCAGCCATTCATTCC
Band lengths:
118-135
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)