HsaINT1015520 @ hg38
Intron Retention
Gene
ENSG00000206503 | HLA-A
Description
major histocompatibility complex, class I, A [Source:HGNC Symbol;Acc:HGNC:4931]
Coordinates
chr6:29944122-29944616:+
Coord C1 exon
chr6:29944122-29944397
Coord A exon
chr6:29944398-29944499
Coord C2 exon
chr6:29944500-29944616
Length
102 bp
Sequences
Splice sites
5' ss Seq
GGGGTAAGG
5' ss Score
8.05
3' ss Seq
ACCTTCCCCTCTTTTCCCAGAGC
3' ss Score
10.92
Exon sequences
Seq C1 exon
ACCCCCCCAAGACACATATGACCCACCACCCCATCTCTGACCATGAGGCCACCCTGAGGTGCTGGGCCCTGGGCTTCTACCCTGCGGAGATCACACTGACCTGGCAGCGGGATGGGGAGGACCAGACCCAGGACACGGAGCTCGTGGAGACCAGGCCTGCAGGGGATGGAACCTTCCAGAAGTGGGCGGCTGTGGTGGTGCCTTCTGGAGAGGAGCAGAGATACACCTGCCATGTGCAGCATGAGGGTCTGCCCAAGCCCCTCACCCTGAGATGGG
Seq A exon
GTAAGGAGGGAGATGGGGGTGTCATGTCTCTTAGGGAAAGCAGGAGCCTCTCTGGAGACCTTTAGCAGGGTCAGGGCCCCTCACCTTCCCCTCTTTTCCCAG
Seq C2 exon
AGCTGTCTTCCCAGCCCACCATCCCCATCGTGGGCATCATTGCTGGCCTGGTTCTCCTTGGAGCTGTGATCACTGGAGCTGTGGTCGCTGCCGTGATGTGGAGGAGGAAGAGCTCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000206503:ENST00000396634:6
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.374 A=NA C2=0.021
Domain overlap (PFAM):
C1:
PF0765410=C1-set=WD(100=93.5),PF066236=MHC_I_C=PU(3.6=1.1)
A:
NA
C2:
PF066236=MHC_I_C=PU(3.6=2.2)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TCTACCCTGCGGAGATCACAC
R:
AGAACCAGGCCAGCAATGATG
Band lengths:
256-358
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Autistic and control brains