HsaINT1015516 @ hg38
Intron Retention
Gene
ENSG00000206503 | HLA-A
Description
major histocompatibility complex, class I, A [Source:HGNC Symbol;Acc:HGNC:4931]
Coordinates
chr6:29941966-29942626:+
Coord C1 exon
chr6:29941966-29942096
Coord A exon
chr6:29942097-29942403
Coord C2 exon
chr6:29942404-29942626
Length
307 bp
Sequences
Splice sites
5' ss Seq
CAGGTAAGG
5' ss Score
11.08
3' ss Seq
CCCTCTCCCAACCTACGTAGGGT
3' ss Score
8
Exon sequences
Seq C1 exon
GCACAACTTTTCCGGATTAAAAACAAAAACAACAACAACAAAAATCTACACCTCCATTCCCAGATCAAGCTTACTCTCTGGCACCAAACTCCATGGGGTGATTTTTCTTCTAGAAGAGTCCAGGTGGACAG
Seq A exon
GTAAGGAGTGGGAGTCAGGGAGTCCAGTTCAGGGACAGAGATAATGGGATGAAAAGTGAAAGGAGAGGGACGGGGCCCATGCCGAGGGTTTCTCCCTTGTTTCTCAGACAGCTCCTGGGCCAAGACTCAGGGAGACATTGAGACAGAGCGCTTCGCACAGGAGCAGAGGGGTCAGGGCGAAGTCCCAGGGCCCCAGGCGTGGCTCTCAGAGTCTCAGGCCCCGAAGGCGGTGTATGGATTGGGGAGTCCCAGCCTTGGGGATTCCCCAACTCCGCAGTTTCTTTTCTCCCTCTCCCAACCTACGTAG
Seq C2 exon
GGTCCTTCATCCTGGATACTCACGACGCGGACCCAGTTCTCACTCCCATTGGGTGTCGGGTTTCCAGAGAAGCCAATCAGTGTCGTCGCGGTCGCTGTTCTAAAGCCCGCACGCACCCACCGGGACTCAGATTCTCCCCAGACGCCGAGGATGGCCGTCATGGCGCCCCGAACCCTCCTCCTGCTACTCTCGGGGGCCCTGGCCCTGACCCAGACCTGGGCGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000206503:ENST00000396634:2
Average complexity
IR
Mappability confidence:
NA
Protein Impact
5' UTR
No structure available
Features
Disorder rate (Iupred):
C1=NA A=NA C2=0.000
Domain overlap (PFAM):
C1:
NA
A:
NA
C2:
PF0012913=MHC_I=PU(0.1=0.0)
Main Skipping Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Mouse
(mm9)
No conservation detected
Cow
(bosTau6)
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:
GCACAACTTTTCCGGATTAAAAACA
R:
GTCTGGGTCAGGGCCAGG
Band lengths:
346-653
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Autistic and control brains