HsaINT0076478 @ hg19
Intron Retention
Gene
ENSG00000237218 | HLA-H
Description
major histocompatibility complex, class I, H (pseudogene) [Source:HGNC Symbol;Acc:4965]
Coordinates
chr6:29857105-29857600:+
Coord C1 exon
chr6:29857105-29857381
Coord A exon
chr6:29857382-29857483
Coord C2 exon
chr6:29857484-29857600
Length
102 bp
Sequences
Splice sites
5' ss Seq
GGGGTAAGG
5' ss Score
8.05
3' ss Seq
ACCTTCCCCCCTTTTCCCAGAGC
3' ss Score
9.87
Exon sequences
Seq C1 exon
ACCCCCCCCAAGACACATATGACCCACCACCCCATCTCTGACCATGAGGCCACCCTGAGGTGCTGGGCCCTGGGCTTCTACCCTGCGGAGATCACACTGACCTGGCAGCGGGATGGGGAGGACCAGACCCAGGACACGGAGCTCGTGGAGACCAGGCCTGCAGGGGATGGAACCTTCCAGAAGTGGGCGGCTGTGGTGGTGCCTTCTGGAGAGGAGCAGAGATACACCTGCCATGTGCAGCATGAGGGTCTGCCCGAGCCCCTCACCCTGAGATGGG
Seq A exon
GTAAGGAGGGAGATGGGGGTGTCATGTCTCTTAGGGAAAGCCGGAGCCTCTCTGGAGAGCTTTAGCAGGGTCAGGGTCCCTCACCTTCCCCCCTTTTCCCAG
Seq C2 exon
AGCCATCTTCCCAGCCCAACGTCCCCATCGTGGGCATCGTTGCTGGCCTGGTTCTACTTGTAGCTGTGGTCACTGGAGCTGTGGTCGCTGCTGTAATGTGGAGGAAGAAGAGCTCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000237218-HLA-H:NR_001434:4
Average complexity
IR-C
Mappability confidence:
NA
Protein Impact
No protein impact description available
No structure available
Features
Disorder rate (Iupred):
C1=NA A=NA C2=NA
Domain overlap (PFAM):
C1:
NA
A:
NA
C2:
NA
Main Inclusion Isoform:
NA
Main Skipping Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Rat
(rn6)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TACCCTGCGGAGATCACACTG
R:
AAGTAGAACCAGGCCAGCAAC
Band lengths:
258-360
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
Other AS DBs:
FasterDB (Includes CLIP-seq data)
AS-ALPS (AS-induced ALteration of Protein Structure, links to PINs)
APPRIS (Selection of principal isoform)
DEU primates (Only for human)