HsaINT0076428 @ hg19
Intron Retention
Gene
ENSG00000223980 | HLA-A
Description
major histocompatibility complex, class I, A [Source:HGNC Symbol;Acc:4931]
Coordinates
chr6:29910309-29910803:+
Coord C1 exon
chr6:29910309-29910403
Coord A exon
chr6:29910404-29910533
Coord C2 exon
chr6:29910534-29910803
Length
130 bp
Sequences
Splice sites
5' ss Seq
CGGGTGAGT
5' ss Score
9.89
3' ss Seq
CAGCCACTGCTCGCCCCCAGGCT
3' ss Score
6.53
Exon sequences
Seq C1 exon
AGATTCTCCCCAGACGCCGAGGATGGCCGTCATGGCGCCCCGAACCCTCCTCCTGCTACTCTCGGGGGCCCTGGCCCTGACCCAGACCTGGGCGG
Seq A exon
GTGAGTGCGGGGTCGGGAGGGAAACCGCCTCTGCGGGGAGAAGCAAGGGGCCCTCCTGGCGGGGGCGCAGGACCGGGGGAGCCGCGCCGGGACGAGGGTCGGGCAGGTCTCAGCCACTGCTCGCCCCCAG
Seq C2 exon
GCTCCCACTCCATGAGGTATTTCTTCACATCCGTGTCCCGGCCCGGCCGCGGGGAGCCCCGCTTCATCGCCGTGGGCTACGTGGACGACACGCAGTTCGTGCGGTTCGACAGCGACGCCGCGAGCCAGAGGATGGAGCCGCGGGCGCCGTGGATAGAGCAGGAGGGGCCGGAGTATTGGGACCAGGAGACACGGAATGTGAAGGCCCAGTCACAGACTGACCGAGTGGACCTGGGGACCCTGCGCGGCTACTACAACCAGAGCGAGGCCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000223980-HLA-A:NM_002116:1
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
Other Inclusion 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:
CGAACCCTCCTCCTGCTACTC
R:
TCACATTCCGTGTCTCCTGGT
Band lengths:
256-386
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)