HsaINT0144194 @ hg19
Intron Retention
Gene
ENSG00000143171 | RXRG
Description
retinoid X receptor, gamma [Source:HGNC Symbol;Acc:10479]
Coordinates
chr1:165377464-165378927:-
Coord C1 exon
chr1:165378795-165378927
Coord A exon
chr1:165377556-165378794
Coord C2 exon
chr1:165377464-165377555
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-RXRG:NM_006917:7
Average complexity
IR-S
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
Other Skipping 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
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)