HsaINT1015586 @ hg38
Intron Retention
Gene
ENSG00000204642 | HLA-F
Description
major histocompatibility complex, class I, F [Source:HGNC Symbol;Acc:HGNC:4963]
Coordinates
chr6:29723306-29723927:+
Coord C1 exon
chr6:29723306-29723527
Coord A exon
chr6:29723528-29723657
Coord C2 exon
chr6:29723658-29723927
Length
130 bp
Sequences
Splice sites
5' ss Seq
CGGGTGAGT
5' ss Score
9.89
3' ss Seq
CAGCCCCTCCTCGCCCCCAGGCT
3' ss Score
8.15
Exon sequences
Seq C1 exon
GTCCTTCTTCCTGGATACTCATAACGCGGCCCCATTTCTCACTCCCATTGGGCGTCGCGTTTCTAGAGAAGCCAATCAGTGTCGCCGCAGTTCCCAGGTTCTAAAGTCCCACGCACCCCGCGGGACTCATATTTTTCCCAGACGCGGAGGTTGGGGTCATGGCGCCCCGAAGCCTCCTCCTGCTGCTCTCAGGGGCCCTGGCCCTGACCGATACTTGGGCGG
Seq A exon
GTGAGTGCGGGGTCCAGAGAGAAACGGCCTCTGTGGGGAGGAGTGAGGGGCCCGCCCGGTGGGGGCGCAGGACTCAGGGAGCCGCCTCCGGAGGAGGGTCTGGCGGGTCTCAGCCCCTCCTCGCCCCCAG
Seq C2 exon
GCTCCCACTCCTTGAGGTATTTCAGCACCGCTGTGTCGCGGCCCGGCCGCGGGGAGCCCCGCTACATCGCCGTGGAGTACGTAGACGACACGCAATTCCTGCGGTTCGACAGCGACGCCGCGATTCCGAGGATGGAGCCGCGGGAGCCGTGGGTGGAGCAAGAGGGGCCGCAGTATTGGGAGTGGACCACAGGGTACGCCAAGGCCAACGCACAGACTGACCGAGTGGCCCTGAGGAACCTGCTCCGCCGCTACAACCAGAGCGAGGCTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000204642:ENST00000376861:2
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=0.055
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
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AGAGAAGCCAATCAGTGTCGC
R:
GGAATTGCGTGTCGTCTACGT
Band lengths:
257-387
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Autistic and control brains