HsaINT0144183 @ hg19
Intron Retention
Gene
ENSG00000186350 | RXRA
Description
retinoid X receptor, alpha [Source:HGNC Symbol;Acc:10477]
Coordinates
chr9:137309004-137313651:+
Coord C1 exon
chr9:137309004-137309173
Coord A exon
chr9:137309174-137313521
Coord C2 exon
chr9:137313522-137313651
Length
4348 bp
Sequences
Splice sites
5' ss Seq
TCGGTGAGT
5' ss Score
11.11
3' ss Seq
CTCTTCTTCCTCCACTGCAGCCG
3' ss Score
9.37
Exon sequences
Seq C1 exon
CCGTGCAGGAGGAGCGGCAGCGTGGCAAGGACCGGAACGAGAATGAGGTGGAGTCGACCAGCAGCGCCAACGAGGACATGCCGGTGGAGAGGATCCTGGAGGCTGAGCTGGCCGTGGAGCCCAAGACCGAGACCTACGTGGAGGCAAACATGGGGCTGAACCCCAGCTCG
Seq A exon
GTGAGTTGCAGCCTGTGCAGGGGTGGGCAGCCTCACATGCCTCAGTTTCCCTCACTCACTCACCCTCCCACCTGAGCAGCTGATGAGCCAGAGAGGTCCTGGGGGCTGCCCTGGGCCCTGTGGCTGCCTCAGCTCGGCCTCTTACCTGAGGTGACCCCGTGGGCCCCTCGCCCCAGCTGGGCGGCACTCTCCTCTCCTGGCCCATGCACGAGTAGCCCATGGGGCAGGGGCCAGGGGCCAGGGGCCCGGGGCCTGGGGCCCTGCGGCCACATCATCATCCTCGGCCACCTCTGCTGGGGCCTCAGCCGCCGTGTCCCCTCGGAGTTTGGCCTGTCTCGGTGCAGAGGCTGTCCCTGCTCCCCGGTGCCACTTGGAAAAGGTATGGGAGGAGGCCGAGCCCCCAGCAAGAGGCTCTGCAGGTTGGTTCCAGGGCTGGCTCTGCCAGCAGCCGTGTGGCCCTGGGCAGGTGCCCGGCAGTCGCGGTGGCTGCTGTTGATACAGGAAGCAGCTCTGCAGCCCCCCAGCTGGTCACCCCCATGCTGACCCTCCTGCCCCCTCCCACCCCAACAGCCTCAAGGGGAGGAGGATTGGGTGGGCCGCAGCCCTGGTCCCGGGCTCTTCTCCTGGGCTGGCTCCAGCTGGTCCTGGAGGTGTTGGATTCAAGACCCCCTGGCCTCGCCCTCCTCTCCTTGGACCCTCCCTGTTACTGGCTCGCTCCCTGTGGCATCTTTGCTTCTGGCTGTGGCCTTGCCAGGGAGGGCAGCACAGGGGCGTTCTGAGCCCCTCCTACCCTACCCTAAGGCCTAGGAACCTGTGCTGCTCGGGAACCATTGCTCCCTGGTGAGCTTGTCTGGCTGGGAGACCCCACCTGTCCCAGGCCCCACTGAGGGGGTGGCTCCAGCTGTGCCCGGGGTTGGGCAGGTGAGCTCCTGGCCACCCGTGTGAAGGTTCAGGACTGTGCAGTAAGCTTCCTGCTGCTGGGGACCTGGGTCCAGCTGGCCCTCAGGGCCCATGTGTCTTTTGCCATGGTCACCATGGTGTCCAGTCTTCATCTGTGTCTCCGTGTGGGTTTGGGGCTGGGACCAGAGCCCTGTGGCCACCGAAGACCTTATACAGGCCGACCATGAGGTTGCCCCAACCTCTGTCCCTCTGTGGGCCCAGGCACACCAGCCTGCCCTCCGTGCTGGGTGCGCCCTGCAGGTCACTGTCTCCCCACCCCCCAGGGCCTTCGTGCTTGCAGCTCACGTGGCCTGGAACTGGGCCCTCTGGCTCTTCCCCAGGCTTTGGTCTCAGCTGAGGTACCTCCGGCCTTCATCTGTGCCCCTGCCAGGGTGGGGACTGCCCCTGTGATGTGGGCTGAGAGCACCTGATCTTTTCTCTGTGGCCCCTGGCACTGGCCACCACAGGGTGAGGTGTGTTCACAGGGTAAGGTGTGTGGTGGGTTAATTTCTGCCCCCACGAGGCTGCTGGTGATGGCTGTGCTGCTCCTCACCACCAGCTTCGGTCAAGGACAGCGACCCCACCCTGCTCGTTGGCACTCACACAAGGCCGGCATCCCCACTGCCTCTGCCTGTCTGAGGGTGGGGGTCTGCTCTTGTCTGAGGCCCCGTGGCTGGGTCAGGGCCACCCTGCTTCCCTGCCCTTTCTGGATAGGACAACCTGGTGCCCCCACGTCCCCGGCTCTGCTCAGACCTCTACTCTGGCTGGGGGCTGGGGCTGCCCAGCTTGGGGGAAGATGAATGGGACCCCGACAGCAGGCACCGTTCTTTCCGGAGAAACCCTCCCCTTGAGTGACAGGCACAGACCCACCCCCAGCCCTGGCTGGTCTGCACGCATGCCCTGCCCTGCTCCCGCCTCACCAGCCTCGCGGAGGGCAGGGGAGGGAGGGTGGCTGTGAGGGTTTCATGATCCAGCAGAAAATCCAAAAGCAAGTTTGGCAGATGCACAAAGGGCTGCCAAGTTTTTATTTCGTGAAGGACATTATTTGGGGGGGAATCTGCCATCTGCTGTCTCCGCCACTGCCTGAAAGTTCAGGGAGTTTAGAACCACAGAGGCAGGCAGGGCTCGCTGGGGATAAAGGACACGTCTTCCACGGGGAGGGGGTCTCTCTGTGCCCGCTCACTCCCTGCTCTGTCTCATCTCACACTGAACGCTCCTCTGTGGACTGGCCTGGGTCCAACTTCCAGAACCGCTCACTGGGCCCCTTCTCTCAGATGGGCAAACTGAGGTCCAGAGAGGGGGCGACCTGCCCAGCGTCACGGTCCTGGTGCCTGGTTTCTCCCCAGCGCGGGGCAGGGCCTGGGCGGGTCCTGTGGACACTTCTAGGCAGGAGTAGAGCCCATCACACGCCTACTGTTACATGAGGCACGTTGGATCTCCAGGCGAGAATGGGAGGCTCACAGAGGTTAATCCTTTCCCCAGGCCACACAGGGAGGTGGAGCCAGGATCCTGCACTATCCCTCCCTACCTAGGGGACCCCCTCCAGGCCTAGCCCTGCTGGTACTGGAGCGAGAGCCTCACACCTGCCGGGAGTGTGCCTCCTCCTCCGCTCCGGCCTCCTGGCTCTCCAGCCTGCCACATTCTGCTCCCTGTGGCCGGCTGTGCACACTGCAGGCACATGACAGATGGTGACCCGTGTGCCCACTCCTGCAGAGGTCCCAGCCAGCCCAGGAGGGCTTGAGGCTCTCCTTCCTACCCATGGCACCAGCCTGTCACCTGGGCCTGCTCTGGGCCCCGTCTTGGCTTCCGAGAGTGGCCGGCTAGTGGCTGGGAAGTTCCTGGGTACAAGGATCCCCAGCAGAGCCACTGCTGCAGACACGGTGCTCGGGGCTGGTTCCCATATCCCCCCGCCCCTGCCAGGCCTGCTTCATCCTTTCTCAGGGATACCCTGCAGCCGATGGGCAGGCGAGAAGGATGGGCCCCTTTCAGCCCCCAGCGTGACAGAAGGAGAGGCTGAGGCTAAGAAGCCAGCCTGGCTGTGGCAGGCCTGGGGGGCGCTGTGCACAGATCCGGGAGCCCTGTGAGTGCTGGGGGCTGTGGCTGCTGCTGATGGAAGGTTTGTGGAGGAATGAGTGAGTCTGTGTAGACTGTGGTCAACCCCACTCAGCCGAGGGATCCCACCCCTGTGTATACCCCTTCTGGCTCGGGCCCCCAAGGGCTGCCCTGCCCTCTTCCGAGGGTCCTGGCGAGTCTCTGTGCCATTCCTCGGGGGCCTTCTCACTCCGCCCTCAGAGGCCTTTCCCGCCGGGCGCTGCGTTTAGGCTGCACGTCTCTGATGAGCAGATGGTTGCTGTTGGTGGAAGCTCTTCAAAGGGAGGCATTTTTCTCCTTGGCAGATGCCCTGAAGTGAGGGATCCCCGAATCCTATTCACAGTCGTTATTCCTGCAGCGGCACCACTGAGGGGGCCGTCATCTGAGTTCCCATTGCTCAGGACACAGAAGGTCCGTGACCCAAGCCCCACCTGCCAGGAGCTGAGGAGGGGCCTCCCCTCCTGCCCTGTTCAAGGCTGCCTGGGTCCCCTCATCTGTGAGACTGAATGGCCCCCTTCCGGCTAGGACTTTCCAAAGGAGCCGTGAATGCTGCTCTCTCTGTGCCTGGGGCCTGGTATCTCAGCCGAGGCTCCTGCCCTCCTGAGCTCCCACATCCATGCCTGATGGAACGTGAGAGGCCAGCCCTGTCCCCAGCGTGGGCCACCTTGGCCATCAGAGATGAAGGTGGTTGGTCCCACCCTGCTCCAGTGCTGCCCATATCCAGTTTCGTCAGCTCGCCGCACCTGCCTTCCAGAGCTGTGGGAGAGACTCGTGCGTCCTGCTGTAACCCAGTGGCTGGAAACAACACACATTTTATTATATGACTGTTCTGTGGCCAGAGAGCCAAAAGCAGTCTTGCCGGGCTGACATCAAGGTGCCTGCCGGCTGGCTCCTGGAGGCTCTGCTGGGGAGTCTGCCCTGGCCTCTGCTTCTGGCACATTCCTTGGCTTGTGGCCTCTTCCTCCACCTTCAAACCCAGCAGTGTCTCTCTCCCCTTGGGCCCCAGCGTCTGTGATCTCATCTCTTCCTCTGACCCTCCTGCCTCCCTCTCATAGACCCCTTGCAATGACCCTGGGTCCCCCCAGTGGTGCAGGCTTACCTCCCAATATCAGGCCACACCTAATCACCTCTGCCAAGCCCCATGTGCCATGCAAGGTCGCATAGTCCCAGGTTCTGGGGATTGGGGCCTGGGCATCTTTGGGGGCCGTATTCAGCGTCCTGCATGGGCCCAGCGTGTGGCAGGGCCTGGTCTGGGCTGTGTTTGGTCAGTACACTGGCTTCTGGGACTGAATGTCCTGCTCTTCTTCCTCCACTGCAG
Seq C2 exon
CCGAACGACCCTGTCACCAACATTTGCCAAGCAGCCGACAAACAGCTTTTCACCCTGGTGGAGTGGGCCAAGCGGATCCCACACTTCTCAGAGCTGCCCCTGGACGACCAGGTCATCCTGCTGCGGGCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000186350-RXRA:NM_002957:5
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.579 A=NA C2=0.114
Domain overlap (PFAM):
C1:
PF0010425=Hormone_recep=PU(4.7=15.8)
A:
NA
C2:
PF0010425=Hormone_recep=FE(22.4=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:
No suggested primer sequences
R:
No suggested primer sequences
Band lengths:
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)