HsaINT0076444 @ hg19
Intron Retention
Gene
ENSG00000239457 | HLA-DOB
Description
major histocompatibility complex, class II, DO beta [Source:HGNC Symbol;Acc:4937]
Coordinates
chr6:32781500-32782378:-
Coord C1 exon
chr6:32782097-32782378
Coord A exon
chr6:32781611-32782096
Coord C2 exon
chr6:32781500-32781610
Length
486 bp
Sequences
Splice sites
5' ss Seq
GGAGTGAGA
5' ss Score
0.49
3' ss Seq
TAAAGACCTGTTTCCCATAGGAG
3' ss Score
6.24
Exon sequences
Seq C1 exon
TGCAACCAGAGGTGACAGTGTACCCAGAGAGGACCCCACTCCTGCACCAGCATAATCTGCTGCACTGCTCTGTGACAGGCTTCTATCCAGGGGATATCAAGATCAAGTGGTTCCTGAATGGGCAGGAGGAGAGAGCTGGGGTCATGTCCACTGGCCCTATCAGGAATGGAGACTGGACCTTTCAGACTGTGGTGATGCTAGAAATGACTCCTGAACTTGGACATGTCTACACCTGCCTTGTCGATCACTCCAGCCTGCTGAGCCCTGTTTCTGTGGAGTGGA
Seq A exon
GTGAGAATTAGTTTCTAGTACTCTCTGGGCCTGACTCAGGACTATACTGACTCAATACAGAGCCTGTGTCACTTCTGCGTTTATCTTGGTCACAACATGAATTATTCTTTCCCTTGATCTGGGACAGTCACAGAAACCAGAGTCCTTGGGTTAGGGTGGGAGAAAACATGGCAGATATCTATCCTCATATCTTCCAAGAAATGAGGAGATCTAATCACCTCATTATGTGCTTCCAACCCTATGAACTGGTGTCCTCTAATTCTTTGGTCTTAGTATTTAGGAGGCATTCTTATGGGCTGTGAGAATCTGTAACCGATGGGGGGTAACTCCATGGGTGCCAACTTTGGTTTCGAAGAACCTTTTCTAAATTTATTTATTTTTCTCTAGCTAGCATTGGATTTGGTGTCTAGTACAGATTCTGGGATTCCAAGAAAGTGCTTTAAATATTGGGATATTTTTACTAATTTAAAGACCTGTTTCCCATAG
Seq C2 exon
GAGCTCAGTCTGAATATTCTTGGAGAAAGATGCTGAGTGGCATTGCAGCCTTCCTACTTGGGCTAATCTTCCTTCTGGTGGGAATCGTCATCCAGCTAAGGGCTCAGAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000239457-HLA-DOB:NM_002120:3
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
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CAGTGTACCCAGAGAGGACCC
R:
TGACGATTCCCACCAGAAGGA
Band lengths:
357-843
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)