HsaINT0115655 @ hg19
Intron Retention
Gene
ENSG00000153234 | NR4A2
Description
nuclear receptor subfamily 4, group A, member 2 [Source:HGNC Symbol;Acc:7981]
Coordinates
chr2:157184916-157186700:-
Coord C1 exon
chr2:157185835-157186700
Coord A exon
chr2:157185046-157185834
Coord C2 exon
chr2:157184916-157185045
Length
789 bp
Sequences
Splice sites
5' ss Seq
AAGGTGAGC
5' ss Score
9.6
3' ss Seq
TATATTGTCTCCTTTTGCAGCGC
3' ss Score
10.74
Exon sequences
Seq C1 exon
CCATGCCTTGTGTTCAGGCGCAGTATGGGTCCTCGCCTCAAGGAGCCAGCCCCGCTTCTCAGAGCTACAGTTACCACTCTTCGGGAGAATACAGCTCCGATTTCTTAACTCCAGAGTTTGTCAAGTTTAGCATGGACCTCACCAACACTGAAATCACTGCCACCACTTCTCTCCCCAGCTTCAGTACCTTTATGGACAACTACAGCACAGGCTACGACGTCAAGCCACCTTGCTTGTACCAAATGCCCCTGTCCGGACAGCAGTCCTCCATTAAGGTAGAAGACATTCAGATGCACAACTACCAGCAACACAGCCACCTGCCCCCCCAGTCTGAGGAGATGATGCCGCACTCCGGGTCGGTTTACTACAAGCCCTCCTCGCCCCCGACGCCCACCACCCCGGGCTTCCAGGTGCAGCACAGCCCCATGTGGGACGACCCGGGATCTCTCCACAACTTCCACCAGAACTACGTGGCCACTACGCACATGATCGAGCAGAGGAAAACGCCAGTCTCCCGCCTCTCCCTCTTCTCCTTTAAGCAATCGCCCCCTGGCACCCCGGTGTCTAGTTGCCAGATGCGCTTCGACGGGCCCCTGCACGTCCCCATGAACCCGGAGCCCGCCGGCAGCCACCACGTGGTGGACGGGCAGACCTTCGCTGTGCCCAACCCCATTCGCAAGCCCGCGTCCATGGGCTTCCCGGGCCTGCAGATCGGCCACGCGTCTCAGCTGCTCGACACGCAGGTGCCCTCACCGCCGTCGCGGGGCTCCCCCTCCAACGAGGGGCTGTGCGCTGTGTGTGGGGACAACGCGGCCTGCCAACACTACGGCGTGCGCACCTGTGAGGGCTGCAAAGGCTTCTTTAAG
Seq A exon
GTGAGCAATGGCGGGAGCGGAGTAGGCAGGTAGGGAGCCCCTAGTGCCCGGGACCTCGGAGTGTGCCCTCTGCCTTGGTGCCAGTAGCCCAGCCCCAGCTCTCCCGGGACTGCCCAGCTCTCCGGGGTCCGCCGAAGCTGCCCTGCAGGAGACCATGGGCTGCGGCGGGGACTTCCGGGTGTCTGAGAAAGGGAAGCAGAAAGACTGGGAGGCCAGGGTCGCATCCCCCTCGCATTCAGCCGACCCGGCTGGCCCCCGCCCGAAGTTGCTGGAGCCGGAGTTGGAAGAGGGTCATTTGCATGTGCTAGGAGCTGTCTTCCCTGTTCAGAATGAAATTGGTTAGGACAGAGAACCGTGTCTGAGCTAACCAAGTGGAACAGAATTCCCTATGGTCAAATTAAGTGATCTCTTTATTTCGCCATCCTGATTGAATAATCTTATCATTTTAAATAGAGAAGGTCTCCAAGGAATGTAAATAATATGAATGCCCACGGATTTGTATTTACTGAGCGTCTCCTTCTCCTTCTCTTGGCATATAAAACACAGCAAGGAGCGGCAAGGTTAGCTCAAATGTTAACGCTATCAATTTTCTTCTGTTAAATGCCCTGGGGGAGGAAAAAAGAAAAGAAAGAAAGAAAAGGAAGAGAAAAAAATAAAATGGAATTGTGTGTATGTGTTTGTTTGTGGGGAGGAATCGTAGACCCCAGTCACATAACAGAAATTTTCTCCGAGTTGCCTGATTTTCAAAAGAAGAAAAAAAATGTTGGTCTATATTGTCTCCTTTTGCAG
Seq C2 exon
CGCACAGTGCAAAAAAATGCAAAATACGTGTGTTTAGCAAATAAAAACTGCCCAGTGGACAAGCGTCGCCGGAATCGCTGTCAGTACTGCCGATTTCAGAAGTGCCTGGCTGTTGGGATGGTCAAAGAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000153234-NR4A2:NM_006186:3
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.536 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0010513=zf-C4=PU(38.6=12.0)
A:
NA
C2:
PF0010513=zf-C4=PD(58.6=93.2)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GACCTTCGCTGTGCCCAAC
R:
TTTGACCATCCCAACAGCCAG
Band lengths:
343-1132
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)