HsaINT1015531 @ hg38
Intron Retention
Gene
ENSG00000204525 | HLA-C
Description
major histocompatibility complex, class I, C [Source:HGNC Symbol;Acc:HGNC:4933]
Coordinates
chr6:31271599-31272086:-
Coord C1 exon
chr6:31271999-31272086
Coord A exon
chr6:31271869-31271998
Coord C2 exon
chr6:31271599-31271868
Length
130 bp
Sequences
Splice sites
5' ss Seq
CCTGTGAGT
5' ss Score
7.21
3' ss Seq
CAGCCCCTCCTCGCCCCCAGGCT
3' ss Score
8.15
Exon sequences
Seq C1 exon
TCCCCAGAGGCCGAGATGCGGGTCATGGCGCCCCGAGCCCTCCTCCTGCTGCTCTCGGGAGGCCTGGCCCTGACCGAGACCTGGGCCT
Seq A exon
GTGAGTGCGGGGTTGGGAGGGAAGCGGCCTCTGCGGAGAGGAGCGAGGGGCCCTCCCGGCGAGGGCGCAGGACCCGGGGAGCCGCGCAGGGAGGTGGGTCGGGCGGGTCTCAGCCCCTCCTCGCCCCCAG
Seq C2 exon
GCTCCCACTCCATGAGGTATTTCGACACCGCCGTGTCCCGGCCCGGCCGCGGAGAGCCCCGCTTCATCTCAGTGGGCTACGTGGACGACACGCAGTTCGTGCGGTTCGACAGCGACGCCGCGAGTCCGAGAGGGGAGCCGCGGGCGCCGTGGGTGGAGCAGGAGGGGCCGGAGTATTGGGACCGGGAGACACAGAAGTACAAGCGCCAGGCACAGGCTGACCGAGTGAGCCTGCGGAACCTGCGCGGCTACTACAACCAGAGCGAGGACG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000204525:ENST00000376228:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.258
Domain overlap (PFAM):
C1:
PF0012913=MHC_I=PU(0.1=0.0)
A:
NA
C2:
PF0012913=MHC_I=PU(50.3=98.9)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
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:
CCCTCCTCCTGCTGCTCTC
R:
TGTCTCCCGGTCCCAATACTC
Band lengths:
242-372
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Autistic and control brains