HsaINT1040776 @ hg38
Intron Retention
Gene
ENSG00000204231 | RXRB
Description
retinoid X receptor beta [Source:HGNC Symbol;Acc:HGNC:10478]
Coordinates
chr6:33198308-33199416:-
Coord C1 exon
chr6:33199169-33199416
Coord A exon
chr6:33198465-33199168
Coord C2 exon
chr6:33198308-33198464
Length
704 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGA
5' ss Score
9.22
3' ss Seq
CCCTATTTCCCCCATCCCAGATT
3' ss Score
7.68
Exon sequences
Seq C1 exon
ACTCCCGAAGCCCAGACAGCTCCTCCCCAAATCCCCTTCCCCAGGGAGTCCCTCCCCCTTCTCCTCCTGGGCCACCCCTACCCCCTTCAACAGCTCCATCCCTTGGAGGCTCTGGGGCCCCACCCCCACCCCCGATGCCACCACCCCCACTGGGCTCTCCCTTTCCAGTCATCAGTTCTTCCATGGGGTCCCCTGGTCTGCCCCCTCCAGCTCCCCCAGGATTCTCCGGGCCTGTCAGCAGCCCCCAG
Seq A exon
GTGAGAGGTTGTGACCAACTTACTGCCTGGCCACTTTCATTTTCTTGTTTTCCTTGTAACCCCAGATCCTTGTGTGAACTTCCCCATGGCCCATTGACCTTCCAATCCTCTAACCTTGTCAGGCCTGTGGTCTTTATGAGACCCCTTGCCTTTCCTGAGGTGACTGATCTTTCAGTGCATGCTTCCTCCCCTAAAAGAACTCTAATATTCTTTGTTTTTGTGTGTGTGTGTGTGTTTTTTTTTTTTTTTTTTTTTGAGATGGAGTCTTGCTCTGTTGCCCAGGCTGGAGTGCAGTGGCACAATCTCAGCTCACTGCAACCTCTGCCTCCTGGGTTCAAGCAATTCTCCTGCCTCAGCCTCCTGAGTAGCTGGGATTACAGGTGCCTACCACCACGCCCGGCTAATTCTGATATTCTTGATGTCCTTTTCATCTATCTGATTTTCTGCCCTTTTGATCCCATCTGCTTTCCCAAGACACCTGCCCTTCAGGGTCACTGTGTTGCACAATTTCAGGGGGGGCCTGTTTATTCACTTTGGGGTTGTGCTCCAGGGATGGCCTTTCACATAGACTGCAGTGTAAATGACAGCCTCTGGAATGTGCATTGCAGGGCCTTGCTTAGTGGTAGGGAATGATTTCCATCACTTCTGTGACATTCTGCTTCCCAATAAGTCTTCCTGTGACTTCCCTATTTCCCCCATCCCAG
Seq C2 exon
ATTAACTCAACAGTGTCACTCCCTGGGGGTGGGTCTGGCCCCCCTGAAGATGTGAAGCCACCAGTCTTAGGGGTCCGGGGCCTGCACTGTCCACCCCCTCCAGGTGGCCCTGGGGCTGGCAAACGGCTATGTGCAATCTGCGGGGACAGAAGCTCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000204231:ENST00000374680:2
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=1.000 A=NA C2=0.757
Domain overlap (PFAM):
C1:
PF118253=Nuc_recep-AF1=PU(58.5=66.3)
A:
NA
C2:
PF118253=Nuc_recep-AF1=PD(39.4=69.8),PF0010513=zf-C4=PU(15.7=20.8)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GAGTCCCTCCCCCTTCTCCTC
R:
GTCCCCGCAGATTGCACATAG
Band lengths:
350-1054
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Autistic and control brains