HsaINT0115650 @ hg19
Intron Retention
Gene
ENSG00000123358 | NR4A1
Description
nuclear receptor subfamily 4, group A, member 1 [Source:HGNC Symbol;Acc:7980]
Coordinates
chr12:52450278-52451043:+
Coord C1 exon
chr12:52450278-52450429
Coord A exon
chr12:52450430-52450840
Coord C2 exon
chr12:52450841-52451043
Length
411 bp
Sequences
Splice sites
5' ss Seq
AAGGTGAGG
5' ss Score
9.16
3' ss Seq
CCACTGGACCGTCTTCCTAGTTC
3' ss Score
4.74
Exon sequences
Seq C1 exon
TTGTCCGAACAGACAGCCTGAAGGGGCGGCGGGGCCGGCTACCTTCAAAACCCAAGCAGCCCCCAGATGCCTCCCCTGCCAATCTCCTCACTTCCCTGGTCCGTGCACACCTGGACTCAGGGCCCAGCACTGCCAAACTGGACTACTCCAAG
Seq A exon
GTGAGGTCCCACCCCGTGTCTGCCTTGGGGAGGTCTATGAGCACATGCAGTGCCTTTGTGCGTGTTAGGAGAGCTACCCCCTCTGGAAGGACTGAATGAGAAAGGAGGTTTAAAAAAGAAAGAAAGAAAAGCGACTCCCTCCAGTTCGACAGATCAAAGAGAGGATCCCCCTCTCGGCTGACCAGATGGGAAAATGCACCCCCTCAGGCAGGTGGCCAATTAGAAAAATATGTCCTTTTGGCAGCTGCAGCCCTGGGTTAATATGTGAGACTTGGCAAGTGAGAGCCTGGGCAGGATCTCAGATCCACTCCCACTCCCGGGATCTGGCATCCAAGTGTCTGACACAGCCATACGTGGCAGTGGGTGTAGGAGCCTGCCTGGGGTGCTGACCCCACTGGACCGTCTTCCTAG
Seq C2 exon
TTCCAGGAGCTGGTGCTGCCCCACTTTGGGAAGGAAGATGCTGGGGATGTACAGCAGTTCTACGACCTGCTCTCCGGTTCTCTGGAGGTCATCCGCAAGTGGGCGGAGAAGATCCCTGGCTTTGCTGAGCTGTCACCGGCTGACCAGGACCTGTTGCTGGAGTCGGCCTTCCTGGAGCTCTTCATCCTCCGCCTGGCGTACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000123358-NR4A1:NM_173157:4
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.353 A=NA C2=0.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0010425=Hormone_recep=PU(31.4=86.8)
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TTGTCCGAACAGACAGCCTGA
R:
GGAGGATGAAGAGCTCCAGGA
Band lengths:
342-753
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)