HsaALTA0004014-3/3 @ hg38
Alternative 3'ss
Gene
ENSG00000204525 | HLA-C
Description
major histocompatibility complex, class I, C [Source:HGNC Symbol;Acc:HGNC:4933]
Coordinates
chr6:31271099-31271868:-
Coord C1 exon
chr6:31271599-31271868
Coord A exon
chr6:31271137-31271348
Coord C2 exon
chr6:31271099-31271136
Length
212 bp
Sequences
Splice sites
5' ss Seq
ACGGTGAGT
5' ss Score
11.45
3' ss Seq
GACCGCGGGGGCGGGGCCAGGGT
3' ss Score
-1.7
Exon sequences
Seq C1 exon
GCTCCCACTCCATGAGGTATTTCGACACCGCCGTGTCCCGGCCCGGCCGCGGAGAGCCCCGCTTCATCTCAGTGGGCTACGTGGACGACACGCAGTTCGTGCGGTTCGACAGCGACGCCGCGAGTCCGAGAGGGGAGCCGCGGGCGCCGTGGGTGGAGCAGGAGGGGCCGGAGTATTGGGACCGGGAGACACAGAAGTACAAGCGCCAGGCACAGGCTGACCGAGTGAGCCTGCGGAACCTGCGCGGCTACTACAACCAGAGCGAGGACG
Seq A exon
GGTCTCACACCCTCCAGAGGATGTCTGGCTGCGACCTGGGGCCCGACGGGCGCCTCCTCCGCGGGTATGACCAGTCCGCCTACGACGGCAAGGATTACATCGCCCTGAACGAGGACCTGCGCTCCTGGACCGCCGCGGACACCGCGGCTCAGATCACCCAGCGCAAGTTGGAGGCGGCCCGTGCGGCGGAGCAGCTGAGAGCCTACCTGGAG
Seq C2 exon
GGCACGTGCGTGGAGTGGCTCCGCAGATACCTGGAGAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000204525-6-9,6-7,6-6-3/3
Average complexity
Alt3
Mappability confidence:
NA
Protein Impact
Protein isoform when splice site is used (Ref)
No structure available
Features
Disorder rate (Iupred):
C1=0.258 A=NA C2=0.202
Domain overlap (PFAM):
C1:
PF0012913=MHC_I=PU(50.3=98.9)
A:
NA
C2:
PF0012913=MHC_I=PD(5.2=27.8)
Other Skipping Isoforms:
NA
Associated events
Conservation
Mouse
(mm9)
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:
ATGAGGTATTTCGACACCGCC
R:
TTCTCCAGGTATCTGCGGAG
Band lengths:
297-509
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Autistic and control brains