HsaALTA0004009-3/4 @ hg38
Alternative 3'ss
Gene
ENSG00000206503 | HLA-A
Description
major histocompatibility complex, class I, A [Source:HGNC Symbol;Acc:HGNC:4931]
Coordinates
chr6:29944500-29945091:+
Coord C1 exon
chr6:29944500-29944616
Coord A exon
chr6:29945041-29945062
Coord C2 exon
chr6:29945063-29945091
Length
22 bp
Sequences
Splice sites
5' ss Seq
CAGGTGGAG
5' ss Score
2.57
3' ss Seq
TCCTTTCTGGTATCTCACAGGAC
3' ss Score
10.34
Exon sequences
Seq C1 exon
AGCTGTCTTCCCAGCCCACCATCCCCATCGTGGGCATCATTGCTGGCCTGGTTCTCCTTGGAGCTGTGATCACTGGAGCTGTGGTCGCTGCCGTGATGTGGAGGAGGAAGAGCTCAG
Seq A exon
GACATTTTCTTCTCACAGATAG
Seq C2 exon
AAAAGGAGGGAGTTACACTCAGGCTGCAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000206503-25-31,25-30,25-29,25-28-3/4
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=0.021 A=NA C2=0.812
Domain overlap (PFAM):
C1:
PF066236=MHC_I_C=PU(3.6=2.2)
A:
NA
C2:
PF066236=MHC_I_C=FE(39.3=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Mouse
(mm10)
No conservation detected
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:
CATCATTGCTGGCCTGGTTCT
R:
GCCTGAGTGTAACTCCCTCCT
Band lengths:
107-129
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Autistic and control brains