HsaINT1040775 @ hg38
Intron Retention
Gene
ENSG00000204231 | RXRB
Description
retinoid X receptor beta [Source:HGNC Symbol;Acc:HGNC:10478]
Coordinates
chr6:33199169-33200688:-
Coord C1 exon
chr6:33200242-33200688
Coord A exon
chr6:33199417-33200241
Coord C2 exon
chr6:33199169-33199416
Length
825 bp
Sequences
Splice sites
5' ss Seq
GGGGTGAGT
5' ss Score
7.93
3' ss Seq
TGTACATACCCCTCCCTCAGACT
3' ss Score
7.23
Exon sequences
Seq C1 exon
GGCGGGAACTCGCGCCGAGACTTCCCGTCTGTACAAAGATGGCTGCCACATTGGCGCTGTCATTTTGGTACTGAGCAGAGCGACGGGCTTAATTCGACCCAATCCAGGCCAGAGTCTTTCTCTCAGGGGCTTCCTCGTGCTCAGCTAATCCTCCGATCAATCCTTGGGAATCCCTGGGACCTCTTCGGTATCCCTACTCTCAGCCAGGGATCATGTCTTGGGCCGCTCGCCCGCCCTTCCTCCCTCAGCGGCATGCCGCAGGGCAGTGTGGGCCGGTGGGGGTGCGAAAAGAAATGCATTGTGGGGTCGCGTCCCGGTGGCGGCGGCGACGGCCCTGGCTGGATCCCGCAGCGGCGGCGGCGGCGGCGGTGGCAGGCGGAGAACAACAAACCCCGGAGCCGGAGCCAGGGGAGGCTGGACGGGACGGGATGGGCGACAGCGGGCGGG
Seq A exon
GTGAGTGCCCCAGCAGAAGGGCAGGCGAGCCAGTGACCGCTTTATCTGCGACCCCTCCCCCACACCCTCCCCCGGTGCTCTTTTCCTTGCGCTCCCGCCCCCTTGTTTGTAAACACGCGTCCCCTCCCTCCCGAGGGCCTTAGCACCCTCCCCCCCGGGGCGGGGCGGGGAAGGGGAGCTTCCGCCCTCCTAGCTGTGACCGCTTGAGGCCTTGGGCACCGGAGGTCGCGGGCCTGGGAAGGGCACGATTCCTCTTAAACCTCAGGACTTTGGGCGTTTACAGGCAGATCCTGCGTCTTAGGAGGGGTCTCTCCTGCCTGTCTCTTTCCCTTGCACGCTCTGGCTACCTGGCTTTACGCTGGGAATAGAGGGGCTCGATGGTCTACCCCACGTGCTGCCCCACCCACGAGACAGGTGTGGCTTTGGGATGACCTGGTATTCATTCAAATGGATTGGTTGGAAAATTTTCCTCACCTGAACTATCCTCCTCTCCTTGTCAACTCCCTCCTCTCACCACAATGAGGAGTTACGCTGTTTTTGGGTTTTTTTAGCCAGTCAAATATAGCAGTGGGAGGTTGTATACCAATTTTAGTGACACAAATGTTAATAAGTTCTGATAACCCACTACCATCGGACCAGCCGGAGTTACACTGTTGTTTGACAGCAGGGTGTCTCTGAACTTGGGGATGGGTGGAGTGGGCTGGGTCCGGCACGGTGGGGTATTAGAGAATTAAAGTCTCTAGTTGGATGTTTGAAGACTCATTTTCTTTTTTTGTCTCTTCTGTCTCTTGTGTGTCTGTGTGCCTGTACATACCCCTCCCTCAG
Seq C2 exon
ACTCCCGAAGCCCAGACAGCTCCTCCCCAAATCCCCTTCCCCAGGGAGTCCCTCCCCCTTCTCCTCCTGGGCCACCCCTACCCCCTTCAACAGCTCCATCCCTTGGAGGCTCTGGGGCCCCACCCCCACCCCCGATGCCACCACCCCCACTGGGCTCTCCCTTTCCAGTCATCAGTTCTTCCATGGGGTCCCCTGGTCTGCCCCCTCCAGCTCCCCCAGGATTCTCCGGGCCTGTCAGCAGCCCCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000204231:ENST00000374680:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.992 A=NA C2=1.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF118253=Nuc_recep-AF1=PU(58.5=66.3)
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:
CCCTACTCTCAGCCAGGGATC
R:
ATGGAGCTGTTGAAGGGGGTA
Band lengths:
355-1180
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Autistic and control brains