HsaINT1015533 @ hg38
Intron Retention
Gene
ENSG00000204525 | HLA-C
Description
major histocompatibility complex, class I, C [Source:HGNC Symbol;Acc:HGNC:4933]
Coordinates
chr6:31270210-31271348:-
Coord C1 exon
chr6:31271073-31271348
Coord A exon
chr6:31270486-31271072
Coord C2 exon
chr6:31270210-31270485
Length
587 bp
Sequences
Splice sites
5' ss Seq
CAGGTACCA
5' ss Score
7.88
3' ss Seq
TTTCTGACTCTTCCCGTCAGAAC
3' ss Score
7.9
Exon sequences
Seq C1 exon
GGTCTCACACCCTCCAGAGGATGTCTGGCTGCGACCTGGGGCCCGACGGGCGCCTCCTCCGCGGGTATGACCAGTCCGCCTACGACGGCAAGGATTACATCGCCCTGAACGAGGACCTGCGCTCCTGGACCGCCGCGGACACCGCGGCTCAGATCACCCAGCGCAAGTTGGAGGCGGCCCGTGCGGCGGAGCAGCTGAGAGCCTACCTGGAGGGCACGTGCGTGGAGTGGCTCCGCAGATACCTGGAGAACGGGAAGGAGACGCTGCAGCGCGCAG
Seq A exon
GTACCAGGGGCAGTGGGGAGCCTTCCCCATCTCCTATAGATCTCCCGGGATGGCCTCCCACGAGGAGGGGAGGAAAATGGGATCAGCACTGGAATATCGCCCTCCCTTGAATGGAGAATGGCATGAGTTTTCCTGAGTTTCCTCTGAGGGCCCCCTCTGCTCTCTAGGACAATTAAGGGATGAAGTCTCTGAGGAAATGGAGGGGAAGACAGTCCCTGGAATACTGATCAGGGGTCTCCTTTGACCACTTTGACCACTGCAGCAGCTGTGGTCAGGCTGCTGACCTTTCTCTCAGGCCTTGTTCTCTGCCTCACACTCAATGTGTCTGAAGGTTTGATTCCAGCTTTTCTGAGTCCTGCAGCCTCCACTCAGGTCAGGACCAGAAGTCGCTGTTCCTCCCTCAGAGACTAGAACTTTCCAATGAATAGGAGATTATCCCAGGTGCCTGTGTCCAGGCTGGCGTCTGGGTTCTCTGCCGCCTTCCCCACCCCAGGTGTCCTGTCCATTCTCAGGATGGTCACATGGGCGCTGCTGGAGTGTCCCAAGAGAGATGCAAAGTGTCTGAATTTTCTGACTCTTCCCGTCAG
Seq C2 exon
AACCCCCAAAGACACACGTGACCCACCACCCCCTCTCTGACCATGAGGCCACCCTGAGGTGCTGGGCCCTGGGCTTCTACCCTGCGGAGATCACACTGACCTGGCAGCGGGATGGGGAGGACCAGACCCAGGACACCGAGCTTGTGGAGACCAGGCCAGCAGGAGATGGAACCTTCCAGAAGTGGGCAGCTGTGGTGGTGCCTTCTGGACAAGAGCAGAGATACACGTGCCATATGCAGCACGAGGGGCTGCAAGAGCCCCTCACCCTGAGCTGGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000204525:ENST00000376228:3
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.184 A=NA C2=0.410
Domain overlap (PFAM):
C1:
PF0012913=MHC_I=PD(49.2=94.6)
A:
NA
C2:
PF0765410=C1-set=WD(100=93.5)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Mouse
(mm9)
No conservation detected
Cow
(bosTau6)
No conservation detected
Chicken
(galGal4)
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:
TTACATCGCCCTGAACGAGGA
R:
GAAGGTTCCATCTCCTGCTGG
Band lengths:
358-945
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Autistic and control brains