HsaINT0144194 @ hg38
Intron Retention
Gene
ENSG00000143171 | RXRG
Description
retinoid X receptor gamma [Source:HGNC Symbol;Acc:HGNC:10479]
Coordinates
chr1:165408227-165409690:-
Coord C1 exon
chr1:165409558-165409690
Coord A exon
chr1:165408319-165409557
Coord C2 exon
chr1:165408227-165408318
Length
1239 bp
Sequences
Splice sites
5' ss Seq
CAGGTGTCT
5' ss Score
2.68
3' ss Seq
TGCTTGTTTCCTGTTAACAGAGT
3' ss Score
7.77
Exon sequences
Seq C1 exon
GGTGGAATGAATTGCTGATTGCCTCTTTCTCCCACCGCTCAGTTTCCGTGCAGGATGGCATCCTTCTGGCCACGGGTTTACATGTCCACCGGAGCAGTGCCCACAGTGCTGGGGTCGGCTCCATCTTTGACAG
Seq A exon
GTGTCTCTCTCCTGCTTCCAGTATTTGTGTGTATTATGTGTGTGTGTGTGTGTGTGTGTGTGTGTATACACATGTGTACATACATGAATTCTCACGTGGGCATGAACCTCTGGGTAGTGCTGGGATGGAGGATGGGCAGCCCAAACAGTTAGCTACACATGACCATGCAGAGACCACTAGGCACATGAAACTATAAACCTGGGGAATGAGGGAGAGATTAAAAGAAAGATTGAGATCACAATAAGATGGAGCCACTCAGAGGCCAGCACAGTTGCCAGGCAGTTGGGAGAACCTATTCTCCCAATGGATTTCCTAAGGAGAGATTAGATCTTGACATCAGCTAGTAAGTTGTGGGTGGAGAGGGTGAACTGTTTATCCTGGGGGCCAAGGATGGGAAAGGGATCAGGATCTGTCCTCAAGAGGCCAGGCAAGATGGACTGTTTATGCTGGGCTCTGGATGATCTCAGAAGGAGGCCTGCAGCAGGAGCAAACCCATCTTCGTCAGGCAGGGATACCCTGACAGAAATTCTGTGCCTTAAATGATACTAAAGGAAAATTAAGCCATCTGATAAGGAGTTGAATAAAATGAGTAGTTAATGACTTGAGAGTGAGAGGATGGAGAACTGGTAAAGAGGAGAATTAAGTTGAAATTAATCTCTCTGTCCAATGCCAGGGCCCCGTTGTCCCTTTCTACCTCCATCGTAAATGGTCTTCTTTGGTCATGTGCACATCCACTGAGCTGTATCTATTACTTCCCTGCCCTTTCCCACATGTTCCATGTAGAGCCCAACATGGTGTTTGGAATGACTCATCCCCCTTCGTGGTAACCGGACCTTTCTACCAGTTCATTGAATGCTGCCCTCTGCTGTGTTTTTCTAGACATGCAATCCCCTTACCTTGCTGTGCCTGTTGCGTTTCTAATTTCCAAGACTTCCATGATGCCTTTCCATTTCCCTGCTTGGAGTTCATTGCTTCCTCTTTGGAACCCACTTGGACTTTGCTCATGGCAGTTATATTCCTGGGCATCGTGCTGCTGCTAGTTTTTAATGTCTGTTTCTTTAGTTAAACTGTAATCTCCTTGCAATGAGGGGTTGCATCTTTTTCATTTCTGTACCCCTAGTAACTGGTACATCATCTGGAAACAGAGTGGGCTTATAAAAATTTTGGTTGAATTCATTTTATTGGCTCTTGGCCTGTTACTTACGGTTTTCTCATTACCTGCTTGTTTCCTGTTAACAG
Seq C2 exon
AGTCCTAACTGAGCTGGTTTCCAAAATGAAAGACATGCAGATGGACAAGTCGGAACTGGGATGCCTGCGAGCCATTGTACTCTTTAACCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000143171:ENST00000359842:7
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0010425=Hormone_recep=FE(22.7=100)
A:
NA
C2:
PF0010425=Hormone_recep=FE(16.0=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GGTGGAATGAATTGCTGATTGCC
R:
GGTTAAAGAGTACAATGGCTCGC
Band lengths:
222-1461
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Autistic and control brains
- Pre-implantation embryo development