HsaINT0076453 @ hg19
Intron Retention
Gene
ENSG00000231939 | HLA-DQB1
Description
major histocompatibility complex, class II, DQ beta 1 [Source:HGNC Symbol;Acc:4944]
Coordinates
chr6:32632575-32634466:-
Coord C1 exon
chr6:32634276-32634466
Coord A exon
chr6:32632845-32634275
Coord C2 exon
chr6:32632575-32632844
Length
1431 bp
Sequences
Splice sites
5' ss Seq
CCGGTAAGT
5' ss Score
10.91
3' ss Seq
CGGCCGGTGATTCCCCGCAGAGG
3' ss Score
7.72
Exon sequences
Seq C1 exon
TTTTTATTCTTTCTGCCAGGTACATCAGATCCATCAGGTCCGAGCTGTGTTGACTACCACTGCTTTTCCCTTCGTCTCAGTTATGTCTTGGAAGAAGGCTTTGCGGATCCCCGGAGACCTTCGGGTAGCAACTGTCACCTTGATGCTGGCGATGCTGAGCTCCCTACTGGCTGAGGGCAGAGACTCTCCCG
Seq A exon
GTAAGTGCAGGGCAGCTGCTCTCCAGAGCCGCCACTCTGGGAACAGGCTCTCCTTGGGCTGGGGTATGGGGGATGGTGATCTCTATGATCTTGGACACAATCTTTCATCAACATTTCCTCTCTCTTGGGAAAGAAAGCTATGTTGCATTCCCATTTATCTTTTAGTGATGAGATGAGGACAATCCAATCCCCATCCTACAGGCTTAAGCCTGGAAGAGGAGGAGAGAGGAGAGAAAGAGGAGATAAAGTGTACATTTACTACCAGCGATAGGACAAAGTGAGCATGGGGTTATTTTTGAAGATATGAATTTCTCCAAAGACACAGCAGGATTTGTCATTTAGGCGTGCCCCAAGACTGCCTGGACTTAGGATTATGAGATCCTGCATTGGAAAATGTGAGGCAGCAATGGTGTCTGTAGTCTCTGTATTTGAGGAAAATTTGTCTCTATTCCTGACCGAGTGGAGCATTTGTGGAGGCAAAATCTTGGTGCTGAGGGAAGCTGACTGGCTGACCACAGAGAGGGAGTCTTCGGGTTTCACTGATTTATGGGCAAATGGTGACTTGAGTGGGATTCAGAGACCCGAGTTAATGGTGGACTGAATTTAGTAGGAAGGAGGATGTAAAGAAGGGAAATAACACATATTGTGAAACCACTCACTTCAGACAGAACAATACTTTATATAACTTCTCTCTCACTCCTTCTAACATCCTGTGTGTAGATATCATGATTTTCTTTTACACAATTATACTTGTGATATGGATATTCTGTTACATAACCTGCCCAAACTGGTGACTGCCACAGTTTAATTGGAATCTAGTTTATCAAATTCAAAAGCTTGTGCTCTTTCCATGAATAAATGTCTCTATCTAGGACTCAGAGGTGTAGGTCCTTTCCAACATAGAAGGGAGTGAACCTCAACGGGACTTGGGAGGGTAAATCTAGGCATGGGAAGGAAGGTATTTTACCCAGGGACCAAGAGAATACGCGTGTCAGAACGAGGCCAGGCTTAATTCCTGGACCTATCTCGTCATTCCGTTGAACTCTCAGATTTATGTGGATAACTTTATCTCTGAGGTATCCAGGAGCTTCATGAAAAATGGGATTTCATGCGAGAACGCCCTGATCCCTCTAAGTGCAGAGGTGCATGTAAAATCAGCCCGACTGCCTCTTCGCTGGGTTCACAGGCTCAGGCAGGGACAGGGCTTTCCTCCCTTTCCTGGATGTAGGAAGGCAGATTCCAGAAGCCCGCAAAGAAGGCGGGCAGAGCTGGGCAGAGCCGCCGGGAGGATCCCAGGTCTGGAGCGCCAGGCACGGGCGGGCGGGAACTGGAGGTCGCGCGGGCGGTTCCACAGCTCCAGGCCGGGTCAGGGCGGCGGCTGCGGGGGCGGCCGGGCTGGGGCCTGACTGACCGGCCGGTGATTCCCCGCAG
Seq C2 exon
AGGATTTCGTGTTCCAGTTTAAGGGCATGTGCTACTTCACCAACGGGACGGAGCGCGTGCGTCTTGTGACCAGATACATCTATAACCGAGAGGAGTACGCGCGCTTCGACAGCGACGTGGGGGTGTACCGCGCGGTGACGCCGCAGGGGCGGCCTGATGCCGAGTACTGGAACAGCCAGAAGGAAGTCCTGGAGGGGACCCGGGCGGAGTTGGACACGGTGTGCAGACACAACTACGAGGTGGCGTTCCGCGGGATCTTGCAGAGGAGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000231939-HLA-DQB1:NM_002123:1
Average complexity
IR-C
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
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:
TGGAAGAAGGCTTTGCGGATC
R:
CCACCTCGTAGTTGTGTCTGC
Band lengths:
346-1777
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development
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)