HsaINT0115662 @ hg19
Intron Retention
Gene
ENSG00000119508 | NR4A3
Description
nuclear receptor subfamily 4, group A, member 3 [Source:HGNC Symbol;Acc:7982]
Coordinates
chr9:102589009-102591275:+
Coord C1 exon
chr9:102589009-102589083
Coord A exon
chr9:102589084-102590322
Coord C2 exon
chr9:102590323-102591275
Length
1239 bp
Sequences
Splice sites
5' ss Seq
TGGGTAAGA
5' ss Score
8.91
3' ss Seq
CCTTTTCTCTGTCCCTGCAGATA
3' ss Score
13.88
Exon sequences
Seq C1 exon
CAGGCCCTCATCACCTTTTTTCAAGTCAAGATTTCATCCCATACATGCATGACTCAATCAGATTTGGAAATGTGG
Seq A exon
GTAAGAGAAAGATGTCAAAGGAAATGTGAAGTATTCACTTCTCTATTAGTCACACCTTTTACACCATAGACTCCAAAGAGGCGTTAAGCACCTGGTTTTCCTTTGGCTCAGAAAAACCAACCACCAAAAACCGCCGTTTTTTACCATTTATATTTAGCCATAAAGAAAGAAAAATAATTAGATAAATCATCCACTACATCCAATAATTCTCAGCGCCTTCTCACTCAGTTCAGCCTCTCTGAACAATAGTAAGCACCCTGGATACCAGCCACTTTGGGGGCAACATAGTCAAACTGGCAGAGAAATCAAGTCTATTGAGAAACTGCTTTTTTTCATGGGTACTAATTCTAGTGTCATAAGGAAATACCTATACTAACTTGCCTATTATGATAGTTATAAACTGTTATCACAAAACAGTCACTGATATGTTTTATTAGTTAGAATTGGGATATATATATGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTATATATATATATATGGGTGGGTGTTTTGTTGCAGCTGCTGATCTTTTTCTTTGCAGATGGTACAAACTCTCCCGAGTCAATTTCCTGGGCCTATGTCCCCACCTAGCTGACTGAAGTTATCAACAGGGGTCCAGTTTGTGCAGGCTGCTAGCCCTATTGGAAGAGTGGGGATGAGGTGGGAGAAAGCAACCACAACGTGTGTGGGCAACCTCAATTGGCACTCATAAAATGTTAGAATGTCAACTCTCTCCCTTGGCCACTAAATCTCTCACAGGGTAGTTTTTCTTGCCTAACTCAGGTTTACAAATCAATGTGTATGCCTTGGGGGACCAATGGCCTCTTTCCTCCCAAATAAACCACTGGCTTTCTCTTTGTCCCCCTAGGTTATAGCTGAGGAGCCCACTCCAATTAGTTTATAGGATTCAAAGCCTCTTTTTAAAAACATCTCTGAGCTTATGAGGAAAGACTTCAAGTTTCCCAAATCTAGTGGAGGACAGGGCAAGGGAGGAAAGATAGGTACAGGAGTCCACAGGAGGCCAGGTTTTGGCACCCCTTTGTCAGGAATTCAGCTTCCTTACTAGGGATGAAGAAAATAAGTGTGGGGCTTTGTGTCTATGCTACCAGAAGGAGGAGAGGATGACACTTCCTCTCTGTTTCCCAGATTAGAGAACAGTGAACCCAATGCTGCCTGTTGGCTAGAAAACAAGTGTTAACTTGCTTCTGAGAGACCCTTTTCTCTGTCCCTGCAG
Seq C2 exon
ATATGCCCTGCGTCCAAGCCCAATATAGCCCTTCCCCTCCAGGTTCCAGTTATGCGGCGCAGACATACAGCTCGGAATACACCACGGAGATCATGAACCCCGACTACACCAAGCTGACCATGGACCTTGGCAGCACTGAGATCACGGCTACAGCCACCACGTCCCTGCCCAGCATCAGTACCTTCGTGGAGGGCTACTCGAGCAACTACGAACTCAAGCCTTCCTGCGTGTACCAAATGCAGCGGCCCTTGATCAAAGTGGAGGAGGGGCGGGCGCCCAGCTACCATCACCATCACCACCACCACCACCACCACCACCACCATCACCAGCAGCAGCATCAGCAGCCATCCATTCCTCCAGCCTCCAGCCCGGAGGACGAGGTGCTGCCCAGCACCTCCATGTACTTCAAGCAGTCCCCACCGTCCACCCCCACCACGCCGGCCTTCCCCCCGCAGGCGGGGGCGTTATGGGACGAGGCACTGCCCTCGGCGCCCGGCTGCATCGCACCCGGCCCGCTGCTGGACCCGCCGATGAAGGCGGTCCCCACGGTGGCCGGCGCGCGCTTCCCGCTCTTCCACTTCAAGCCCTCGCCGCCGCATCCCCCCGCGCCCAGCCCGGCCGGCGGCCACCACCTCGGCTACGACCCGACGGCCGCTGCCGCGCTCAGCCTGCCGCTGGGAGCCGCAGCCGCCGCGGGCAGCCAGGCCGCCGCGCTTGAGAGCCACCCGTACGGGCTGCCGCTGGCCAAGAGGGCGGCCCCGCTGGCCTTCCCGCCTCTCGGCCTCACGCCCTCCCCTACCGCGTCCAGCCTGCTGGGCGAGAGTCCCAGCCTGCCGTCGCCGCCCAGCAGGAGCTCGTCGTCTGGCGAGGGCACGTGTGCCGTGTGCGGGGACAACGCCGCCTGCCAGCACTACGGCGTGCGAACCTGCGAGGGCTGCAAGGGCTTTTTCAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000119508-NR4A3:NM_173200:1
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=0.000 A=NA C2=0.532
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0253517=Zip=WD(100=34.6),PF0010513=zf-C4=PU(38.6=8.5)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TCATCCCATACATGCATGACTCA
R:
GTGGTGGTGGTGATGGTGATG
Band lengths:
347-1586
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)