HsaALTA0004015-2/5 @ hg38
Alternative 3'ss
Gene
ENSG00000204525 | HLA-C
Description
major histocompatibility complex, class I, C [Source:HGNC Symbol;Acc:HGNC:4933]
Coordinates
chr6:31269495-31270085:-
Coord C1 exon
chr6:31269966-31270085
Coord A exon
chr6:31269517-31269525
Coord C2 exon
chr6:31269495-31269516
Length
9 bp
Sequences
Splice sites
5' ss Seq
CAGGTAGGG
5' ss Score
9.46
3' ss Seq
AGGGCATTTTCTTCCCACAGGTG
3' ss Score
9.73
Exon sequences
Seq C1 exon
AGCCATCTTCCCAGCCCACCATCCCCATCATGGGCATCGTTGCTGGCCTGGCTGTCCTGGTTGTCCTAGCTGTCCTTGGAGCTGTGGTCACCGCTATGATGTGTAGGAGGAAGAGCTCAG
Seq A exon
GTGGAAAAG
Seq C2 exon
GAGGGAGCTGCTCTCAGGCTGC
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000204525-17-24,17-23,17-22,17-21,17-19-2/5
Average complexity
Alt3
Mappability confidence:
NA
Protein Impact
Protein isoform when splice site is used (Ref)
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.071
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 Skipping Isoforms:
NA
Associated events
Conservation
Cow
(bosTau6)
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:
TGGCTGTCCTGGTTGTCCTAG
R:
AGCCTGAGAGCAGCTCCC
Band lengths:
92-101
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Autistic and control brains