HsaINT0076439 @ hg19
Intron Retention
Gene
ENSG00000206435 | HLA-C
Description
major histocompatibility complex, class I, C [Source:HGNC Symbol;Acc:4933]
Coordinates
chr6:31238850-31239645:-
Coord C1 exon
chr6:31239376-31239645
Coord A exon
chr6:31239126-31239375
Coord C2 exon
chr6:31238850-31239125
Length
250 bp
Sequences
Splice sites
5' ss Seq
ACGGTGAGT
5' ss Score
11.45
3' ss Seq
GACCGCGGGGGCGGGGCCAGGGT
3' ss Score
-1.7
Exon sequences
Seq C1 exon
GCTCCCACTCCATGAGGTATTTCGACACCGCCGTGTCCCGGCCCGGCCGCGGAGAGCCCCGCTTCATCTCAGTGGGCTACGTGGACGACACGCAGTTCGTGCGGTTCGACAGCGACGCCGCGAGTCCGAGAGGGGAGCCGCGGGCGCCGTGGGTGGAGCAGGAGGGGCCGGAGTATTGGGACCGGGAGACACAGAAGTACAAGCGCCAGGCACAGGCTGACCGAGTGAGCCTGCGGAACCTGCGCGGCTACTACAACCAGAGCGAGGACG
Seq A exon
GTGAGTGACCCCGGCCCGGGGCGCAGGTCACGACCCCTCCCCATCCCCCACGGACGGCCCGGGTCGCCCAGAGTCTCCCCGTCTGAGATCCACCCCAAGGTGGATCTGCGGAACCCGCCCAGACCCTCGACCGGAGAGAGCCCCAGTCGCCTTTACCCGGTTTCATTTTCGGTTTAGGCCAAAATCCCCGCGGGTTGGTCGGGGCGGGGCGGGGCTCGGGGGACTGGGCTGACCGCGGGGGCGGGGCCAG
Seq C2 exon
GGTCTCACACCCTCCAGAGGATGTCTGGCTGCGACCTGGGGCCCGACGGGCGCCTCCTCCGCGGGTATGACCAGTCCGCCTACGACGGCAAGGATTACATCGCCCTGAACGAGGACCTGCGCTCCTGGACCGCCGCGGACACCGCGGCTCAGATCACCCAGCGCAAGTTGGAGGCGGCCCGTGCGGCGGAGCAGCTGAGAGCCTACCTGGAGGGCACGTGCGTGGAGTGGCTCCGCAGATACCTGGAGAACGGGAAGGAGACGCTGCAGCGCGCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000206435-HLA-C:NM_002117:2
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:
GCTTCATCTCAGTGGGCTACG
R:
TCGTAGGCGGACTGGTCATAC
Band lengths:
295-545
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)