HsaINT1015565 @ hg38
Intron Retention
Gene
ENSG00000179344 | HLA-DQB1
Description
major histocompatibility complex, class II, DQ beta 1 [Source:HGNC Symbol;Acc:HGNC:4944]
Coordinates
chr6:32659467-32661457:-
Coord C1 exon
chr6:32661347-32661457
Coord A exon
chr6:32660250-32661346
Coord C2 exon
chr6:32659467-32660249
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
GGCTTCTGCACTGACTCCTGAGACTATTTTAACTAGGATTGGTTATCACTCTTCTGTGATGCCTGCTTATGCCTGCCCAGAATTCCCAGCTGCCTGTGTCAGCTTGTCCCCCTGAGATCAAAGTCCTACAGTGGCTGTCACGCAGCCACCAGGTCATCTCCTTTCATCCCCACCCCAAGGCGCTGGCTGTGACTCTGCTTCCTGCACTGACCCAGAGCCTCTGCCTGTGCATGGCCAGCTGCGTCTACTCAGGTCCCAAGGGGTTTCTGTTTCTATTCTTTCCTCAGACTGCTCAAGAGAAGCACATGAAAAACATTACCTGACTTTAGAGCTTTTTTACATAATTAAACATGATCCTGAGTTATCTGTATTCTGAACTTTCTTAATTGAGAAGAGGCAGGAAATCACTGCAGAATGAAGGAACATCCCTTGAGGTGACCCAGCAAACCTGTGGCCAGAAGGAGGATTGTACCTTGAAAAGACACTGAAAGCATTTTGGGGTGTGAAGTAAGGGTGGGCAGAGGAGGTAGAAAATAATTCAATTGTCGCATCATTCATGGTTCTTTAATACTGATGCTCAGTGCATTGGCCTTAGAATATCCCAGCCTCTCTTCTGGTTTGGTGAGTGCTGTGTAAATAAGCATGGTAGAATTGTTTGGAGACATATATAGTGATCCTTGGTCACTGGTGTTTCAAACATTCTGGAAAGTCACATCGATCAAGAATATTTTTTATTTTTAAGAAAGCATAACCAGCAATAAAAATACTATTTTTGAGTCTAAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000179344:ENST00000434651:4
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.009 A=NA C2=0.200
Domain overlap (PFAM):
C1:
PF0765410=C1-set=PD(9.3=23.7)
A:
NA
C2:
NO
Main Inclusion Isoform:
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:
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
- Autistic and control brains