HsaINT1015587 @ hg38
Intron Retention
Gene
ENSG00000204642 | HLA-F
Description
major histocompatibility complex, class I, F [Source:HGNC Symbol;Acc:HGNC:4963]
Coordinates
chr6:29723658-29724448:+
Coord C1 exon
chr6:29723658-29723927
Coord A exon
chr6:29723928-29724172
Coord C2 exon
chr6:29724173-29724448
Length
245 bp
Sequences
Splice sites
5' ss Seq
CTGGTGAGT
5' ss Score
10.1
3' ss Seq
TGACTGCGGGGACCGGCTAGGGT
3' ss Score
-0.4
Exon sequences
Seq C1 exon
GCTCCCACTCCTTGAGGTATTTCAGCACCGCTGTGTCGCGGCCCGGCCGCGGGGAGCCCCGCTACATCGCCGTGGAGTACGTAGACGACACGCAATTCCTGCGGTTCGACAGCGACGCCGCGATTCCGAGGATGGAGCCGCGGGAGCCGTGGGTGGAGCAAGAGGGGCCGCAGTATTGGGAGTGGACCACAGGGTACGCCAAGGCCAACGCACAGACTGACCGAGTGGCCCTGAGGAACCTGCTCCGCCGCTACAACCAGAGCGAGGCTG
Seq A exon
GTGAGTGAACCCGGCCGGGGGCGCAGGTCACGACCACCCCCCATCCGCCACGGACCGCCCGGGTCCCTCAGAGTCTCCGGATCCGAAATCTACCCCGAGGCAGCGGGACCCGCCCAGACCCTCCACCCGGGAGAGTCCCAGGCGCCTTTACCCAGGTTCATTTTCAGTTTAGGCCAAAATCCCCGCGGGTTGGGCGGGGAGGGGGCGGGGCTAGCTGGGCGGGGCTGACTGCGGGGACCGGCTAG
Seq C2 exon
GGTCTCACACCCTCCAGGGAATGAATGGCTGCGACATGGGGCCCGACGGACGCCTCCTCCGCGGGTATCACCAGCACGCGTACGACGGCAAGGATTACATCTCCCTGAACGAGGACCTGCGCTCCTGGACCGCGGCGGACACCGTGGCTCAGATCACCCAGCGCTTCTATGAGGCAGAGGAATATGCAGAGGAGTTCAGGACCTACCTGGAGGGCGAGTGCCTGGAGTTGCTCCGCAGATACTTGGAGAATGGGAAGGAGACGCTACAGCGCGCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000204642:ENST00000376861:3
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.055 A=NA C2=0.148
Domain overlap (PFAM):
C1:
PF0012913=MHC_I=PU(50.3=98.9)
A:
NA
C2:
PF0012913=MHC_I=PD(49.2=94.6)
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:
CGTAGACGACACGCAATTCCT
R:
GGTCCTCGTTCAGGGAGATGT
Band lengths:
308-553
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Autistic and control brains