HsaINT0076456 @ hg19
Intron Retention
Gene
ENSG00000231939 | HLA-DQB1
Description
major histocompatibility complex, class II, DQ beta 1 [Source:HGNC Symbol;Acc:4944]
Coordinates
chr6:32627657-32629234:-
Coord C1 exon
chr6:32629124-32629234
Coord A exon
chr6:32628027-32629123
Coord C2 exon
chr6:32627657-32628026
Length
1097 bp
Sequences
Splice sites
5' ss Seq
AAGGTGAGG
5' ss Score
9.16
3' ss Seq
TGCTCTTCTCTCTTCTCCAGGGC
3' ss Score
12.49
Exon sequences
Seq C1 exon
GGGCTCAGTCTGAATCTGCCCAGAGCAAGATGCTGAGTGGCGTTGGAGGCTTCGTGCTGGGGCTGATCTTCCTTGGGCTGGGCCTTATCATCCGTCAAAGGAGTCAGAAAG
Seq A exon
GTGAGGAACCCCAGGGGAAAAGGGGAAGATGGGCTGTGACCCAGACCCTCTGTTCAGAGTGGTCCTGTCTGTAGATTAGCTCTTTCCTCCTGACCCTGAGAAGAAGTGCGAGGAGACAGGACAAGATGGGAGGAGGCATTGGAATCTGATTTTACTGGTTGAAAGGTAGCGCTGTCACAGAGCTGACTGATAGAGCTTATTCCAGGGCATCCTTACCATTCATCATTGTCTCACTGGCTCCTTTCCAAAAGCTTCCTCCATTAAGAGGGTCAGAGCCTCAGCTTCCTTTCTTTCTAGTGACAATTTCCTTTGTTTTAGGGGATTTTAAATTAGGGTGCTGAAGGCCTGGAAGAACATGGGTGGGAAGAGAATGTAACTCTAAGTCATGTGTGTCATTTTCCTTTGGGGTGAGAGAGTGGCTGTTTGTGTAATGAGACCTTTCTCTGCATAACTTCCTTTTGTAAGACCTCAAGGGCCTCCACCAGCAGGTAATATTTCAGCCATGATCCAGTGTGGGGAGGCACAGGTATAAGAGGGAAGAGCATGAGCTGAGTGTACCTGACCACAGTGGTCCATGTTCATGGCCTATTTGCTGCTATGAGGATCAAGACTTAGGGGAGAAGTTTGCCAGTTTCTAGGAATCTCCAGACATTGTTCCCCAGAACCAAGCCTTAACTTTGGTGGCATCTTCTTGTGAAATGTGGAGCCAGAACCACAGCTTAAATGTTAGACACTAGGATGATGCCCACTTTGTGCCACATGATGGTGGCTACTGCCTGTAAGCATTTTCCAGTGACTGAAAGAGGCTGCTAGTGGTCGGGAAGAGATATCATCCAATTTCCTAAAAAGACTGAACCCTTCATATTCCCCAGAAGAATAACAGCTGTTCCCCACCTCCCACACATCTGCATCAAGCTGAAGTTCTGTGTCCTCATGAGCTGATTTCACCTTTGCACAGATCTTGGGGGAGGTGATGACAATACACCCTGGACCTCAACTTTCTCTGTCTGAAGCTGCAGGGGGCCCCTGAAGGGTGGGGGAGATGGCAGGCCCACCAGGATACCCTGTGCTGATCAATGCTCTTCTCTCTTCTCCAG
Seq C2 exon
GGCTTCTGCACTGACTCCTGAGACTATTTTAACTAGGATTGGTTATCACTCTTCTGTGATGCCTGCTTATGCCTGCCCAGAATTCCCAGCTGCCTGTGTCAGCTTGTCCCCCTGAGATCAAAGTCCTACAGTGGCTGTCACGCAGCCACCAGGTCATCTCCTTTCATCCCCACCCCAAGGCGCTGGCTGTGACTCTGCTTCCTGCACTGACCCAGAGCCTCTGCCTGTGCATGGCCAGCTGCGTCTACTCAGGTCCCAAGGGGTTTCTGTTTCTATTCTTTCCTCAGACTGCTCAAGAGAAGCACATGAAAAACATTACCTGACTTTAGAGCTTTTTTACATAATTAAACATGATCCTGAGTTATCTGTA
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000231939-HLA-DQB1:NM_002123:4
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
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
Associated events
Conservation
Rat
(rn6)
No conservation detected
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AAGATGCTGAGTGGCGTTGG
R:
TTGGGACCTGAGTAGACGCAG
Band lengths:
344-1441
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)