HsaINT1040773 @ hg38
Intron Retention
Gene
ENSG00000186350 | RXRA
Description
retinoid X receptor alpha [Source:HGNC Symbol;Acc:HGNC:10477]
Coordinates
chr9:134371971-134374130:+
Coord C1 exon
chr9:134371971-134372139
Coord A exon
chr9:134372140-134374006
Coord C2 exon
chr9:134374007-134374130
Length
1867 bp
Sequences
Splice sites
5' ss Seq
GAGGTGTGG
5' ss Score
4.48
3' ss Seq
TTTTCTCTGCCTGTTTGTAGCCC
3' ss Score
9.28
Exon sequences
Seq C1 exon
CTGGGTGCCAGGCCCAGCCTGGGCCTCCCTTGTGGGGTGCTCAGGCCCCACTTCCCTCCCTGGGGAGGGGAGGAGAGGCCACCTCGAGGGAGTGACGTCAAGGCAGGGTGACATTAGTCTGGGCCCACGGGATCCTTGCTACTTCCCCATTTATGGAGGGGAAACTGAG
Seq A exon
GTGTGGAGAGGGGTGAGGATGGGTTTGAAGCCCGGCCATCCAGTCTCAGTGCCGCTTGTAGAGGCAGAAGGGCGTAGGGAGGGAGAGGGAGAGCCAGGTAGGCCGAAGGCGCCTGGCAGTGTGGCAGGACACGCGCCCACTGGGGAGGTGGAGGGCCGCAGCCAGGGCCTCAGCTGAGGGCCTCCTGGATGCTGGCTTTGCTGTTGGGGCTGGAGCATGGACCCGTCCTGGGCCGATTATGGGAGATGGTGTGGAGTGGGGGCCGCAGGCGAGGGTCCCTCTTCCTTTGGCTGGAGGAGGCCTGGCCCTGGGACTGTCCCGTGAGGGGAGACAGTGGTTGGACCCATTGCAGAATTGATTTGTTATCACTGGGTTCCAGGCACACGGCTTAGAGGGCATCACGGAGGCCTCCCCGTCACCTCAGAGGGCATCACGGAGGCCTCCCCATCATCTTATGGGGTGGGTGTTATTAGGCTTAGTTTAGAGGAGACAGAGGATCAGAGAGGCCCACTGACCCGCCTTGGGGCCCCCAGCAGGCAGAGGAACTGTGTCCAGGTGCTGGACTGTGAGACCCTGCTCTTCCCGGGACTCTACCACCTCAGAGGGTGGCAGCACAGGGCCCAGCAGGGCGTGTGCTCCTGTGGGGCAGGCGAGTCCTGGCTCTGCCCTTGTAGGCTGTGTGACCCCAGGCGGTAGCTCAGGCTCTCTGGTCTGGACTGGGCGCGGAGCTGCTTGAGATCTGGAATCTGGCTTTCTGGTGAAGGGGCAGCAGGAGAGGGGCTGAGACCCAGCCTTCCTGGTTGCAGAGCTGCGGTAGGCCAGACCCTCCTGCCTGCTGGGTGGGGCCTGGCATTCCAGGAACCTGTGGTCAAGCCTGGCCTGGGCTGTGGCGTCTGCCCCGGGTTCGTCAGCAGGGGAGGGGCCCTGGAGACCAGTCCGTTATGGATGAGGAAGCGGGTGCCCAGAGAGGGTGAGGAGCTGGGCTGGGCCACACAGCCAAGTGGCCACAGAGCTGGGGGTGGTCAGGAGCCATGCTTTCTGGTAAGGCGGAAGTGTCTGGGGCCCGGGTGGGATGAAGGACTCGGGTCCCAGAGACCAGCCTTTGGTGCTGTTCTTGGGCTAGGAATGGCAGTAACAGGAAGGGCATGGCCACCGAGACGCACTGAGTTATGGGCACCTGCCGTCTGCCAGGAACTGTGGTCCACGCCCGACTGTCTTTAACAGCTCTGTGCCTGCTGCTGTGTGCCGGGCCCTGCGCTCAGCCCTTCTCGTGTGTGGTCTCCAACCCTGTGTTTTCCCAGGCCGTTGGCCCATTTTCCAGATGAGAATACTGCGGCCCAGAGAAGCAGCATTGTGTGCTGCGGTCCTTGGCCACGAGGTGGTGTGGGTTTTTTTGACCCAGATCTTCCTGTCTATCACCCTCCCTGGGCCTACCTTCCTTATGGTAGACACATGTGCAGGTCTGTCCCATCCCCCAGCTATCCACAGAGAGGCCAGGGTTTGGCATGGGGAGGTGTCGGAGCCTACTGGGTTGTAGCTGGAGGGAGGTGAGTGGCACCTCCCACAGGAAGCCCCCCTTGATGTCTCCTCCACCTTGCCACATTACCAGCCGATAGCCAGGTTCCTGGAAAAGGCTGTCTTTCTGACTCTGGACTGGGTGCCCCTGGGCAGGGCCCACCTTTGTTTTCTAATTTATTTTAATTAAAAATTTAAAAATTAGAGACAGAGTCTTGCTTTGTTGCCCAGGCTAGACGTGAACTCCTGGGCTCAAGTGATCCTCCCGCCCCGGCCTCTCGGGTAGTGGGGACTTCAGGAGTGCGCCACCTCACCTGGCCTCCCAGCCTGGTTTTTCTCTGCCTGTTTGTAG
Seq C2 exon
CCCTGGGTTCGACGGGGGAAGCAGTCGCCTGATGGGCAAGTGCTCTCTGAGTGGTGCATGAAGGTGGCTGTCCACGTGGCTGTCTGTGGTGTCGGTTAATCGTCACGGCTTCCGGGAGTTAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000186350:ENST00000356384:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
5' UTR
No structure available
Features
Disorder rate (Iupred):
C1=NA A=NA C2=NA
Domain overlap (PFAM):
C1:
NA
A:
NA
C2:
NA
Main Inclusion Isoform:
NA
Main Skipping Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Mouse
(mm9)
No conservation detected
Cow
(bosTau6)
No conservation detected
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CAGCCTGGGCCTCCCTTG
R:
CTTTAACTCCCGGAAGCCGTG
Band lengths:
279-2146
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Autistic and control brains