HsaINT1015564 @ hg38
Intron Retention
Gene
ENSG00000179344 | HLA-DQB1
Description
major histocompatibility complex, class II, DQ beta 1 [Source:HGNC Symbol;Acc:HGNC:4944]
Coordinates
chr6:32664798-32666694:-
Coord C1 exon
chr6:32666499-32666694
Coord A exon
chr6:32665068-32666498
Coord C2 exon
chr6:32664798-32665067
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
ACAGGTTTTTATTCTTTCTGCCAGGTACATCAGATCCATCAGGTCCGAGCTGTGTTGACTACCACTGCTTTTCCCTTCGTCTCAGTTATGTCTTGGAAGAAGGCTTTGCGGATCCCCGGAGACCTTCGGGTAGCAACTGTCACCTTGATGCTGGCGATGCTGAGCTCCCTACTGGCTGAGGGCAGAGACTCTCCCG
Seq A exon
GTAAGTGCAGGGCAGCTGCTCTCCAGAGCCGCCACTCTGGGAACAGGCTCTCCTTGGGCTGGGGTATGGGGGATGGTGATCTCTATGATCTTGGACACAATCTTTCATCAACATTTCCTCTCTCTTGGGAAAGAAAGCTATGTTGCATTCCCATTTATCTTTTAGTGATGAGATGAGGACAATCCAATCCCCATCCTACAGGCTTAAGCCTGGAAGAGGAGGAGAGAGGAGAGAAAGAGGAGATAAAGTGTACATTTACTACCAGCGATAGGACAAAGTGAGCATGGGGTTATTTTTGAAGATATGAATTTCTCCAAAGACACAGCAGGATTTGTCATTTAGGCGTGCCCCAAGACTGCCTGGACTTAGGATTATGAGATCCTGCATTGGAAAATGTGAGGCAGCAATGGTGTCTGTAGTCTCTGTATTTGAGGAAAATTTGTCTCTATTCCTGACCGAGTGGAGCATTTGTGGAGGCAAAATCTTGGTGCTGAGGGAAGCTGACTGGCTGACCACAGAGAGGGAGTCTTCGGGTTTCACTGATTTATGGGCAAATGGTGACTTGAGTGGGATTCAGAGACCCGAGTTAATGGTGGACTGAATTTAGTAGGAAGGAGGATGTAAAGAAGGGAAATAACACATATTGTGAAACCACTCACTTCAGACAGAACAATACTTTATATAACTTCTCTCTCACTCCTTCTAACATCCTGTGTGTAGATATCATGATTTTCTTTTACACAATTATACTTGTGATATGGATATTCTGTTACATAACCTGCCCAAACTGGTGACTGCCACAGTTTAATTGGAATCTAGTTTATCAAATTCAAAAGCTTGTGCTCTTTCCATGAATAAATGTCTCTATCTAGGACTCAGAGGTGTAGGTCCTTTCCAACATAGAAGGGAGTGAACCTCAACGGGACTTGGGAGGGTAAATCTAGGCATGGGAAGGAAGGTATTTTACCCAGGGACCAAGAGAATACGCGTGTCAGAACGAGGCCAGGCTTAATTCCTGGACCTATCTCGTCATTCCGTTGAACTCTCAGATTTATGTGGATAACTTTATCTCTGAGGTATCCAGGAGCTTCATGAAAAATGGGATTTCATGCGAGAACGCCCTGATCCCTCTAAGTGCAGAGGTGCATGTAAAATCAGCCCGACTGCCTCTTCGCTGGGTTCACAGGCTCAGGCAGGGACAGGGCTTTCCTCCCTTTCCTGGATGTAGGAAGGCAGATTCCAGAAGCCCGCAAAGAAGGCGGGCAGAGCTGGGCAGAGCCGCCGGGAGGATCCCAGGTCTGGAGCGCCAGGCACGGGCGGGCGGGAACTGGAGGTCGCGCGGGCGGTTCCACAGCTCCAGGCCGGGTCAGGGCGGCGGCTGCGGGGGCGGCCGGGCTGGGGCCTGACTGACCGGCCGGTGATTCCCCGCAG
Seq C2 exon
AGGATTTCGTGTTCCAGTTTAAGGGCATGTGCTACTTCACCAACGGGACGGAGCGCGTGCGTCTTGTGACCAGATACATCTATAACCGAGAGGAGTACGCGCGCTTCGACAGCGACGTGGGGGTGTACCGCGCGGTGACGCCGCAGGGGCGGCCTGATGCCGAGTACTGGAACAGCCAGAAGGAAGTCCTGGAGGGGACCCGGGCGGAGTTGGACACGGTGTGCAGACACAACTACGAGGTGGCGTTCCGCGGGATCTTGCAGAGGAGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000179344:ENST00000434651:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.020
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0096914=MHC_II_beta=WD(100=81.3)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Chicken
(galGal3)
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
- Autistic and control brains