HsaINT0115687 @ hg19
Intron Retention
Gene
ENSG00000148200 | NR6A1
Description
nuclear receptor subfamily 6, group A, member 1 [Source:HGNC Symbol;Acc:7985]
Coordinates
chr9:127284703-127287152:-
Coord C1 exon
chr9:127287000-127287152
Coord A exon
chr9:127285073-127286999
Coord C2 exon
chr9:127284703-127285072
Length
1927 bp
Sequences
Splice sites
5' ss Seq
CAGGTAACA
5' ss Score
8.88
3' ss Seq
TTCTCCCCCCTTGTTCCCAGGAA
3' ss Score
9.49
Exon sequences
Seq C1 exon
ATATCAGGGGTCTGACCAGTGCCTCACAGCTGGAACAATTGAATAAACGATACTGGTACATTTGCCAGGATTTTACTGAATATAAATACACACATCAGCCGAACCGCTTTCCTGATCTCATGATGTGCTTACCTGAGATTCGATATATTGCAG
Seq A exon
GTAACATTCTGGGTCTTGGGCTCCCAACCCTTCCTTGCTTCTCTTAGCTTGTGAAGGGAATGAGGCAAGCAGTGTTTTCAGGGTGCTCTTTCCAGCCCATCACCAACTGCATGAAAGAGTTCTCACCCTTGCCCTCAAAAAAGGTCTGTTATAATGAGAAGCTTGCATTCTCCATAGAGAAGAGAAGTTAATTTCCTGAGCTCTTATGATATGCAGGGTACTTTGTGGCCTTATATCATTTAATCTCATACCAGTCTCCGCTGGTGGTTGGCAATATTATAGCCATTTTATGGATGAGGAAACAGAGACTCAGAGTATCTCAAATTAACTTAATTTCTTGAATTGTGTACTTTAAAAGAGTGAATTTTATGATACATGAATTATATCTCAATTTTTAAAATTATCTTAATTTCACAGAATTTCCCATGAGCTTTGAGGGATCATTTATTTAAAGTGATATCTTTAGCTGGGCACAGTGGCTCCTGCCTGTAATCCCAGCTACTCAGGAGGCTGGGGCGAGAGGATCAGTTGAGGCTAGGAGTTAAGACCAGCCTGGGCAACATAGTGAGACCTCATCTCTAAAAAATTTAAAATAAGAATAGGAAAAATAAAGTTTAAAATCCTGTATTTGCAGAGGAATTTTATGTATTGGGGTGTGTGTGTATGTATGTATGTTTCTATGTGGTCTTGACCCCTTCTGAGCTTTCTGACATTTAAATAGGTCTATTTCAATATAAAATCCTGGCTTTTTTGGTTGTTGCCTTGCTTCATGTGGTAAAGATTCTTGTTCTGGCTGTCCAGCAGATACTGAGGGGCAGCTCAGAAATGTGACCTATAGACCGGGATTCTTCCTGTAAAATTCAGCAATACAGTTTTTTAATTCAACATAAAAATTCTGGAGAAAGCAATACGATTTTAAAGGAAAATTATTTCAATCTGACAAGGGAATTTTTTTTTCTATTTCTTGGGCCACAAAGCAGTCTAGCAAATGTGAGCTGGGCCTAAACTATTGGAATTTTAGGGATATTTTGACAGTTTGTCTCAGTATTTTCTAAGCTAGAGTTTACCACATGAGATATTAAGCAGGCACTCTGTGAAATAAAAGGAAGTCAACAATTACATGCCACTCTCCTCCATAGAACTGGGTCCTCAGCCTTGGCGGCACTTCCAATCACCTGGAAAACTTAAAAAAAAAAAAAAAATCAATGTTTGAGTTGCACCTGGAGAATTCTGGTTTAATTGGAATGGGGTAGAGCCTGGAGATAATCAGTGTTTTCGAACGGCTCCCCAGGTCACTCAGAGGTACTGTTTGCCAGAAGAAACACAGCCTTAGGTATTTATAAATTATATTAGCACACTGAATGCTCTGAGAAGTCCTTCAATCAAGAAATCTGTAAAGCTCTTTTAACCCTGAGTTTCTCAAATGTATTTGCCTCTTTACCCCTGCTTCTTTTTCCCCTAGTACTTTTATTAACCTATTAAACCATTCTGAAGTGCAATATTTTATAGAATATTACTTAGAAAATCTACCGGGGGTTGAGGGGGTGAAGAAAACAGGACAGAAGTTTTTTGGACTACCTGTCAGTTTCAGCTTCCTTATCTATAAAATGAGGGTAAAAAGTAGTACACAGAAATAGTGTGAGAATTCAACGAGGTAATGCATTTAACCACCTAGAACAGAGTTAAGTATTCCCTGAGTAGTAGAATGATGATGAGTTGGCACCATTACTAGGCTCCCTGGGCACCCAAAGGGGTCTGGATGTTAGGATGTTAGCCCAGTGTGTCCAACCTTTGTGATACTCCTGGCACTTCTCTTGCCCCAGTCACTCAGCAAGGTGATACTCTGCCTCCACCAGCCCAAGGAGGCTGACTTGCCTGTCCACTAGAGTGACCACTGCTAACTCTTCTTCTCCCCCCTTGTTCCCAG
Seq C2 exon
GAAAGATGGTGAATGTGCCCCTGGAGCAGCTGCCCCTCCTCTTTAAGGTGGTGCTGCATTCCTGCAAGACCAGTGTGGGCAAGGAATGACCTGTTCCAGGCGCCCTCCTCAGGCCAACCACAGCGTCTTGGGTGGGCAGGACAGGCTCTGGAGGGAAAAGCCAGAGAGACCAAGATGGAGGCTGTGGAGCAGCATTTCCCGTTGCCTCCATAGCAAGAAGAGTTTTTGTTTGTTTGTCTGTTTTTTTAACCTCATTTTTCTATATATTTATTTCACGACAGAGTTGAATGTATGGCCTTCAACATGATGCACATGCTTTTGTGTGAATGCAGCCAATGCATTTTCTTACAGTTTACAGAATGTGAAGATG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000148200-NR6A1:NM_033334:9
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0010425=Hormone_recep=FE(26.4=100)
A:
NA
C2:
PF0010425=Hormone_recep=PD(8.8=56.7)
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:
GTGCCTCACAGCTGGAACAAT
R:
TATGGAGGCAACGGGAAATGC
Band lengths:
347-2274
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Genotype-Tissue Expression Project (GTEx)
- 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)