HsaALTA1055969-1/2 @ hg38
Alternative 3'ss
Gene
ENSG00000204525 | HLA-C
Description
major histocompatibility complex, class I, C [Source:HGNC Symbol;Acc:HGNC:4933]
Coordinates
chr6:31270439-31272050:-
Coord C1 exon
chr6:31271073-31272050
Coord A exon
NA
Coord C2 exon
chr6:31270439-31270485
Length
0 bp
Sequences
Splice sites
5' ss Seq
CAGGTACCA
5' ss Score
7.88
3' ss Seq
TTTCTGACTCTTCCCGTCAGAAC
3' ss Score
7.9
Exon sequences
Seq C1 exon
GTCACGACCCCTCCCCATCCCCCACGGACGGCCCGGGTCGCCCAGAGTCTCCCCGTCTGAGATCCACCCCAAGGTGGATCTGCGGAACCCGCCCAGACCCTCGACCGGAGAGAGCCCCAGTCGCCTTTACCCGGTTTCATTTTCGGTTTAGGCCAAAATCCCCGCGGGTTGGTCGGGGCGGGGCGGGGCTCGGGGGACTGGGCTGACCGCGGGGGCGGGGCCAGGGTCTCACACCCTCCAGAGGATGTCTGGCTGCGACCTGGGGCCCGACGGGCGCCTCCTCCGCGGGTATGACCAGTCCGCCTACGACGGCAAGGATTACATCGCCCTGAACGAGGACCTGCGCTCCTGGACCGCCGCGGACACCGCGGCTCAGATCACCCAGCGCAAGTTGGAGGCGGCCCGTGCGGCGGAGCAGCTGAGAGCCTACCTGGAGGGCACGTGCGTGGAGTGGCTCCGCAGATACCTGGAGAACGGGAAGGAGACGCTGCAGCGCGCAG
Seq A exon
NA
Seq C2 exon
AACCCCCAAAGACACACGTGACCCACCACCCCCTCTCTGACCATGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000204525-9-12,9-11-1/2
Average complexity
Alt3
Mappability confidence:
NA
Protein Impact
Protein isoform when splice site is used (Ref)
No structure available
Features
Disorder rate (Iupred):
C1=0.202 A=NA C2=0.432
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
Mouse
(mm9)
No conservation detected
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:
CAGATCACCCAGCGCAAGTT
R:
CTCATGGTCAGAGAGGGGGTG
Band lengths:
174-249
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Autistic and control brains