HsaINT0115649 @ hg19
Intron Retention
Gene
ENSG00000123358 | NR4A1
Description
nuclear receptor subfamily 4, group A, member 1 [Source:HGNC Symbol;Acc:7980]
Coordinates
chr12:52449814-52450429:+
Coord C1 exon
chr12:52449814-52449943
Coord A exon
chr12:52449944-52450277
Coord C2 exon
chr12:52450278-52450429
Length
334 bp
Sequences
Splice sites
5' ss Seq
AAGGTGTGT
5' ss Score
6.64
3' ss Seq
CCCTACCCATTCCTTTGCAGTTG
3' ss Score
9.21
Exon sequences
Seq C1 exon
CGCACAGTGCAGAAAAACGCCAAGTACATCTGCCTGGCTAACAAGGACTGCCCTGTGGACAAGAGGCGGCGAAACCGCTGCCAGTTCTGCCGCTTCCAGAAGTGCCTGGCGGTGGGCATGGTGAAGGAAG
Seq A exon
GTGTGTGGCTGGGGTGCGGCCCAGCGGGGCAAGGGTAGGCTTGAGTGGAGTGGGACCAGCAGGGCCCCCAGGCTTCTGCCCTGGAGGACCCAGAGGAGGGCACGTCTTATTTCCACCCCACCTCTGAACCCCAGGCCTTGGAGGGAGGCAGCCTACACCTGCCTGGATTGTGAGGGTGGTGGCAGGGGGAGGTTCCTATAGGGTACCTTGGATCTCAGGGACTCTGGGTCCTAGGGACTCGGTGGGGCGCGTCTCAGCAGTGGTGTGCACGGCTTGGGCTGAGAGGCCCTTCCTCAGATCCCTTCCTTCCTCACCCCTACCCATTCCTTTGCAG
Seq C2 exon
TTGTCCGAACAGACAGCCTGAAGGGGCGGCGGGGCCGGCTACCTTCAAAACCCAAGCAGCCCCCAGATGCCTCCCCTGCCAATCTCCTCACTTCCCTGGTCCGTGCACACCTGGACTCAGGGCCCAGCACTGCCAAACTGGACTACTCCAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000123358-NR4A1:NM_173157:3
Average complexity
IR-C
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.353
Domain overlap (PFAM):
C1:
PF0010513=zf-C4=PD(58.6=93.2)
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GCACAGTGCAGAAAAACGCC
R:
GGAGTAGTCCAGTTTGGCAGTG
Band lengths:
278-612
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)