HsaINT0115657 @ hg19
Intron Retention
Gene
ENSG00000153234 | NR4A2
Description
nuclear receptor subfamily 4, group A, member 2 [Source:HGNC Symbol;Acc:7981]
Coordinates
chr2:157183230-157184526:-
Coord C1 exon
chr2:157184363-157184526
Coord A exon
chr2:157183433-157184362
Coord C2 exon
chr2:157183230-157183432
Length
930 bp
Sequences
Splice sites
5' ss Seq
AGGGTAAGA
5' ss Score
9.21
3' ss Seq
TTTTTAAAATGAAATTCCAGTTC
3' ss Score
3.59
Exon sequences
Seq C1 exon
TGGTTCGCACAGACAGTTTAAAAGGCCGGAGAGGTCGTTTGCCCTCGAAACCGAAGAGCCCACAGGAGCCCTCTCCCCCTTCGCCCCCGGTGAGTCTGATCAGTGCCCTCGTCAGGGCCCATGTCGACTCCAACCCGGCTATGACCAGCCTGGACTATTCCAGG
Seq A exon
GTAAGAAGCTGGCGGGGGGGATATCATGTGGACAAACCGACAGATGGGCAGGACCCCTCCCCACATCCGTCATTAACTCTCAGATTCAACGGGGGTAAAGAAGGCAAGCAAGGCTGTATATGCCTCGCAGCTCTGGCCAGGGCCTCAAGATTCAGATCTTCAGACAATCCATGTAGCTGGGGGCATAGACATGAGGACAGGATGGAGGAAGGAGGAGAGGGACACGCCACAGGGTTTGAAGCTGTGTGAATTCCCACTACCCCACTACCCCATCGCCCCTCCTCTTCCATATACACCAGTGCCTCTACCATGAAATCCAGGGGCTGTGCAAACTCTCCCCCTTCCCAATCTACTTTATTCCCAGTCCTCCATAGAGATAGATGCTTTAATCCTCATCCTTCCTGGCACTGTGCTGGGGAAGGATGTGGGGGCCTGTCTGGGGGTCAGGGAAGGGAAGGAGAGGGTGTAAAGAATGCCAGTGGGGTGGGGGATCAAGTGGTCAGATCCTTTTTACTCCAGCTGTGAAAAATATGCGGGCTTTAATTGGAGGAAGTATGTTGAGCAAACCTGGTAGGGACTGCAATTTTATTAAGATTTGCAAAAGGGCGTCTCAGCTCGAGGCCCACTCTGGGACTAGCATGAATACTAACATGTCAATTGTTTTGTGGAGATAAGAGTGAACGTTTCCCAGGGCTGGATGGCACTGTATTTAGTCTGTATGGAAATGGCAATTTACATATTTAAAGCAGCGACCTCGTAGCACCATCCCTAATTGAATTAATTGCCCCGGAACATCTAATTTCCTTACTGGTCAGAGAGAGGTTTAATTGTTATAAAAACCTGGCTCCCCTATTAGAAACGGGGTTAGCAATTTCACGGGTTATATATTTTAGAGAACCTCATTAAGTGCTTTTTAAAATGAAATTCCAG
Seq C2 exon
TTCCAGGCGAACCCTGACTATCAAATGAGTGGAGATGACACCCAGCATATCCAGCAATTCTATGATCTCCTGACTGGCTCCATGGAGATCATCCGGGGCTGGGCAGAGAAGATCCCTGGCTTCGCAGACCTGCCCAAAGCCGACCAAGACCTGCTTTTTGAATCAGCTTTCTTAGAACTGTTTGTCCTTCGATTAGCATACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000153234-NR4A2:NM_006186:5
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.483 A=NA C2=0.019
Domain overlap (PFAM):
C1:
PF0010425=Hormone_recep=PU(0.5=1.8)
A:
NA
C2:
PF0010425=Hormone_recep=FE(33.8=100)
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:
GCACAGACAGTTTAAAAGGCCG
R:
TGCTAATCGAAGGACAAACAGT
Band lengths:
356-1286
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)