HsaINT0115653 @ hg19
Intron Retention
Gene
ENSG00000153234 | NR4A2
Description
nuclear receptor subfamily 4, group A, member 2 [Source:HGNC Symbol;Acc:7981]
Coordinates
chr2:157187180-157189287:-
Coord C1 exon
chr2:157188992-157189287
Coord A exon
chr2:157187304-157188991
Coord C2 exon
chr2:157187180-157187303
Length
1688 bp
Sequences
Splice sites
5' ss Seq
TAAGTGAGT
5' ss Score
6.43
3' ss Seq
TTCCTGTGTCTGTATTTCAGGGA
3' ss Score
11.23
Exon sequences
Seq C1 exon
GCTGACGCGCGCTGACGCGCGGAGACTTTAGGTGCATGTTGGCAGCGGCAGCGCAAGCCACATAAACAAAGGCACATTGGCGGCCAGGGCCAGTCCGCCCGGCGGCTCGCGCACGGCTCCGCGGTCCCTTTTGCCTGTCCAGCCGGCCGCCTGTCCCTGCTCCCTCCCTCCGTGAGGTGTCCGGGTTCCCTTCGCCCAGCTCTCCCACCCCTACCCGACCCCGGCGCCCGGGCTCCCAGAGGGAACTGCACTTCGGCAGAGTTGAATGAATGAAGACAGACGCGGAGAACTCCTAA
Seq A exon
GTGAGTAGATGCAGCCCATGCAGTTCGCCTTCTTTTATGCTTTTTCCTTCTTTTGCACGTCTCTTCTTTCCACTTGTGTGGGACAGGTTCTCTGGAAGTGGGAGCCAGAGGCTTCTAGTGAGAGTGGGACCGAAGGATGGGGAGTGCGTGCGCGCAGTTACCGGGGGGCATTTGTTCGAACTCCGGCTTTGGCACTAGTGGGGAGTTGGCTCTCGACAGAGGTTTCCAGGCTCCTCATTGGTGGACGTGGAAGGGAGACTCCACAGTTTGGGAGCTGAGGACTAGCCCGCGGAAATGTGCGCAAAGTTTGCTGTTAGTGAGGAATTGATTGTGGCCTGTGAACACGGAGACTCCAAGTCCTATGTATACGAGGGAAGCTGCCCACAAACTGACAGGGAGAGGAAGTTCTTCAGTTTATGCGTTGCTTGGGAACTGTGTCTCCGCGGCTGGCCAGCGCGCGATGTTTCCCGGGTATTGTTGAGTAAGGGTGGTGTTGGTAGCGTGTCCTGTTACTAAGTTGCCTGAAATTTCTGGTTTTGACATATGCTGTCCTTGGGTTTGCGAATGTATCAGAGCGAGAATATGAATATGTAAAGAGTACAGTTATGAAACTGTGGAGCTACCAGGGGGTTAATATCCAACACAGGAATATCTCTAAGGGCTGTGGGGTTCGAGTCTCCTTTCTGCTTTTTCTGGGTAATCTTCCCCCCACCCCCACCACCACTATGAAGCAAGATTGTGGGGGAGGGGAAAGAATAAAAAGAGAGGATACTGGCTTTCTTTTTTCATTAGTAATAAGATTGTCTGTGCTCTAGAATGTCTTCCAAGTGGGAACATCTGAAAATTGCTAGGACACAAGAATGCCTTGTTCCAGAAAGGCAGATTGTGGAAGGCATTATGGGGAAGGTGTTCATCTTGCTGTGCTGGGAAACACTTCTAATATTGGTGCCAATACCATATAAGCAGTATGTCCCCCCTCTGCAATTGACCTAAGAAGCTCCTGGAAAAGTAGATCCCCTCTTCCCACCTTGTGACCATTAAGCCTTGTGACCATTAAAGATGCTGAAAGACAAGTTTTCTGGAAAAGTGAACATCAATTTATCTGTAGCTCCAATCCCAGTGCTCTGTCAAAAGCACTTTAGAAGTGCGGATGCTTCCACTCAACTTGCCTTCTCAGTCAAGGCCTTTCTAACATTTTGTAAGGGGGAAGATTGTTTTCTCATTTTATATTCTTGACTTCTACTTTCTTCCCCTCTACCAAAAGAAAAGGCAATTTCACCACAAGAAAAAAAAATGCAAGAGAAGGTTCCAATGCTGTATTTTCATACTCTAGTCTTCATACTCAGGTCCTGAATTAACCTAAGATGGAAATGACCTCTCCACCTACACTGTAGCAAAGGGGCCAGTTCATTACATCATAAATGTTAAATGAGTTCATGGACTAGCTTTCCTCTTGCAGGATCTTCTCTCTGCAAGGATTTACACAGTGCAATGGGTGGTATTTTCTGTTGTTTCAAGTCATTTCTTTTATACATTCATTTTAAGTGCTATGTTTGGTAAAGGCTTCCCACTCATTTCCAATGAGACAAACAGGGAAGGCATGGAAGGGCCTGCCTGGTGAGTCTACATATGCCCAGCTGAATCTCTGTCGGGAAGAAACCCTGAAGCTTCCTGTGTCTGTATTTCAG
Seq C2 exon
GGAGGAGATTGGACAGGCTGGACTCCCCATTGCTTTTCTAAAAATCTTGGAAACTTTGTCCTTCATTGAATTACGACACTGTCCACCTTTAATTTCCTCGAAAACGCCTGTAACTCGGCTGAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000153234-NR4A2:NM_006186:1
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
5' UTR
No structure available
Features
Disorder rate (Iupred):
C1=NA A=NA C2=NA
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CACATAAACAAAGGCACATTGGC
R:
AGCCGAGTTACAGGCGTTTTC
Band lengths:
358-2046
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)