HsaINT0115648 @ hg19
Intron Retention
Gene
ENSG00000123358 | NR4A1
Description
nuclear receptor subfamily 4, group A, member 1 [Source:HGNC Symbol;Acc:7980]
Coordinates
chr12:52448111-52449943:+
Coord C1 exon
chr12:52448111-52448988
Coord A exon
chr12:52448989-52449813
Coord C2 exon
chr12:52449814-52449943
Length
825 bp
Sequences
Splice sites
5' ss Seq
AAGGTACCG
5' ss Score
9.67
3' ss Seq
CGTGTTGCCCCCCCACCCAGCGC
3' ss Score
6.99
Exon sequences
Seq C1 exon
AGATGCCCTGTATCCAAGCCCAATATGGGACACCAGCACCGAGTCCGGGACCCCGTGACCACCTGGCAAGCGACCCCCTGACCCCTGAGTTCATCAAGCCCACCATGGACCTGGCCAGCCCCGAGGCAGCCCCCGCTGCCCCCACTGCCCTGCCCAGCTTCAGCACCTTCATGGACGGCTACACAGGAGAGTTTGACACCTTCCTCTACCAGCTGCCAGGAACAGTCCAGCCATGCTCCTCAGCCTCCTCCTCGGCCTCCTCCACATCCTCGTCCTCAGCCACCTCCCCTGCCTCTGCCTCCTTCAAGTTCGAGGACTTCCAGGTGTACGGCTGCTACCCCGGCCCCCTGAGCGGCCCAGTGGATGAGGCCCTGTCCTCCAGTGGCTCTGACTACTATGGCAGCCCCTGCTCGGCCCCGTCGCCCTCCACGCCCAGCTTCCAGCCGCCCCAGCTCTCTCCCTGGGATGGCTCCTTCGGCCACTTCTCGCCCAGCCAGACTTACGAAGGCCTGCGGGCATGGACAGAGCAGCTGCCCAAAGCCTCTGGGCCCCCACAGCCTCCAGCCTTCTTTTCCTTCAGTCCTCCCACCGGCCCCAGCCCCAGCCTGGCCCAGAGCCCCCTGAAGTTGTTCCCCTCACAGGCCACCCACCAGCTGGGGGAGGGAGAGAGCTATTCCATGCCTACGGCCTTCCCAGGTTTGGCACCCACTTCTCCACACCTTGAGGGCTCGGGGATACTGGATACACCCGTGACCTCAACCAAGGCCCGGAGCGGGGCCCCAGGTGGAAGTGAAGGCCGCTGTGCTGTGTGTGGGGACAACGCTTCATGCCAGCATTATGGTGTCCGCACATGTGAGGGCTGCAAGGGCTTCTTCAAG
Seq A exon
GTACCGCGCAGCCCCAGGTGGGGCCTTTTGTTGGAAATGGAGAGAGGCTGGCCTCATCCCATTGGGACCTGTGGTCTCCCCCTGGGTTCTCCTCCTAGCTAAGTCCTGTCCTGCAGGGTGGGATCAGCCCTGCCAGGTGGGCCGCCTTCCTGGAGACCCGTAGATGCCAGGGCTGGAAGCTTTCATTTGCCGGGACACTCGGGCCCATGGGATTGCACAGAGCTGGAGGGAGGGGTGAGATAGGGGCAGATAGGAGCTGCAGGGGTGCCTGGCGAGCCTCTGGTTTTCCTCTGCTCCTCTGCCTGTCCTCTCCCAACTCAAGGTTCTAGTGGGAAGGGGTGCCCCCAGGCTCTCATGTTCCTGGCGTGAGATGAAAGGATCCCTGCGGAGGGTTTGGTTCTTGAGGGCTGGGGGTGGACTTGGGAACAGGCTGTGTGTTTGTCCCAGCGATGGTGCCTGCTTAGCTTCCCGTCCCCACCCCCCAGCCCCTTGGCCCTCTCCTGTCTGCCCTAGGGAGAAGGCAGGTGGACAAGGGCCCATGAAAAAATACAGGTGTCTAGACTGCCAGGGAGACCCTGGCCCCCAGTAGTGTGTCCTGGGGACTTCCTCAGAGCGAGAAACCTCCCCCAATGTCTTCAAGACTTTTCTCTCCCCCCGCCCAACCCCGTCTCTCCCTCCCTTGCCACCCAAATGTTAGAAAAATAGCTGTGAACAGAGAGCGCTTTTGTCTGCAATGGCAGCAGGATCTGGACGGTCCCCTCCCCTAAGTTCCCCCCTCCCCACCCCACACTCTGACAGCTTGTTCCGTGTTGCCCCCCCACCCAG
Seq C2 exon
CGCACAGTGCAGAAAAACGCCAAGTACATCTGCCTGGCTAACAAGGACTGCCCTGTGGACAAGAGGCGGCGAAACCGCTGCCAGTTCTGCCGCTTCCAGAAGTGCCTGGCGGTGGGCATGGTGAAGGAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000123358-NR4A1:NM_173157:2
Average complexity
IR-C
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.575 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0010513=zf-C4=PU(38.6=9.2)
A:
NA
C2:
PF0010513=zf-C4=PD(58.6=93.2)
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GCCTCCAGCCTTCTTTTCCTT
R:
CAGGCAGATGTACTTGGCGTT
Band lengths:
358-1183
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)