HsaALTA0004015-2/2 @ hg19
Alternative 3'ss
Gene
ENSG00000204525 | HLA-C
Description
major histocompatibility complex, class I, C [Source:HGNC Symbol;Acc:4933]
Coordinates
chr6:31237272-31237862:-
Coord C1 exon
chr6:31237743-31237862
Coord A exon
chr6:31237303-31237320
Coord C2 exon
chr6:31237272-31237302
Length
18 bp
Sequences
Splice sites
5' ss Seq
CAGGTAGGG
5' ss Score
9.46
3' ss Seq
TCCTCCCAGTCCCCTCATAGGGC
3' ss Score
5.29
Exon sequences
Seq C1 exon
AGCCATCTTCCCAGCCCACCATCCCCATCATGGGCATCGTTGCTGGCCTGGCTGTCCTGGTTGTCCTAGCTGTCCTTGGAGCTGTGGTCACCGCTATGATGTGTAGGAGGAAGAGCTCAG
Seq A exon
GGCATTTTCTTCCCACAG
Seq C2 exon
GTGGAAAAGGAGGGAGCTGCTCTCAGGCTGC
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000204525-9-10,9-9-2/2
Average complexity
Alt3
Mappability confidence:
NA
Protein Impact
Protein isoform when splice site is used (No Ref)
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.067
Domain overlap (PFAM):
C1:
PF126692=P12=PU(53.6=73.2),PF066236=MHC_I_C=PU(6.9=4.9)
A:
NA
C2:
PF126692=P12=FE(19.6=100),PF066236=MHC_I_C=FE(37.9=100)
Other Inclusion Isoforms:
NA
Associated events
Conservation
Mouse
(mm10)
No conservation detected
Mouse
(mm9)
No conservation detected
Rat
(rn6)
No conservation detected
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GTTGCTGGCCTGGCTGTC
R:
TGAGAGCAGCTCCCTCCTTTT
Band lengths:
107-125
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)