HsaINT0076455 @ hg19
Intron Retention
Gene
ENSG00000231939 | HLA-DQB1
Description
major histocompatibility complex, class II, DQ beta 1 [Source:HGNC Symbol;Acc:4944]
Coordinates
chr6:32629124-32630025:-
Coord C1 exon
chr6:32629744-32630025
Coord A exon
chr6:32629235-32629743
Coord C2 exon
chr6:32629124-32629234
Length
509 bp
Sequences
Splice sites
5' ss Seq
GGCGTAAGG
5' ss Score
4.88
3' ss Seq
CACTCAGTTCTGCTCTTTAGGGG
3' ss Score
6.13
Exon sequences
Seq C1 exon
TGGAGCCCACAGTGACCATCTCCCCATCCAGGACAGAGGCCCTCAACCACCACAACCTGCTGGTCTGCTCGGTGACAGATTTCTATCCAGGCCAGATCAAAGTCCGGTGGTTTCGGAATGATCAGGAGGAGACAGCCGGCGTTGTGTCCACCCCCCTTATTAGGAATGGTGACTGGACTTTCCAGATCCTGGTGATGCTGGAAATGACTCCCCAGCGTGGAGATGTCTACACCTGCCACGTGGAGCACCCCAGCCTCCAGAGCCCCATCACCGTGGAGTGGC
Seq A exon
GTAAGGGGATATTGAGTTTCTGTTACTATGGGCCCACAAGACAAAGAGCTCCTTCTGACCCATTCCTTCCCATCTCTTATCCCTGATGTCACTACTGAGCTGGGAATCACAGGAGACTAGAGCACCTCTTGCTCCATGGCAAGTGCATCAGAAGAATCCTGGTCTCATCACCTTTCCAGATGCTAGGGAAATTACTCTACATACTGTTGCTCTGAATCCCAGTCCTGATAGCTCTGAGGGACTGATTCTTAGGGCTGGTGACTGGGATCTTAGGGTCTAAGGTTATGGATGAGTTCTTGAAGAGCAGAGATTTGCTTCCCCACTCTCTCACCTATTCACTGTATCCAAGGACCTATTGGCTGGTCTTTCCCCTCCTTAGGGGTGGTCTGAATGGAGAACTAGGTTCCTTTGATGCCTTCACCTTCTGCACCTCAGACTGGACTTCAACTCCTCAGCAGGGATGCTATGGGGTGTGGGGACAAACACAGACACTCAGTTCTGCTCTTTAG
Seq C2 exon
GGGCTCAGTCTGAATCTGCCCAGAGCAAGATGCTGAGTGGCGTTGGAGGCTTCGTGCTGGGGCTGATCTTCCTTGGGCTGGGCCTTATCATCCGTCAAAGGAGTCAGAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000231939-HLA-DQB1:NM_002123:3
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:
AGTGACCATCTCCCCATCCAG
R:
AAGGAAGATCAGCCCCAGCA
Band lengths:
346-855
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)