HsaINT0115674 @ hg19
Intron Retention
Gene
ENSG00000116833 | NR5A2
Description
nuclear receptor subfamily 5, group A, member 2 [Source:HGNC Symbol;Acc:7984]
Coordinates
chr1:200012902-200014712:+
Coord C1 exon
chr1:200012902-200013020
Coord A exon
chr1:200013021-200014570
Coord C2 exon
chr1:200014571-200014712
Length
1550 bp
Sequences
Splice sites
5' ss Seq
AAGGTTTGC
5' ss Score
5.42
3' ss Seq
CTATTTTCTCTGTCTTATAGGGA
3' ss Score
11.04
Exon sequences
Seq C1 exon
TGTCTCAATTTAAAATGGTGAATTACTCCTATGATGAAGATCTGGAAGAGCTTTGTCCCGTGTGTGGAGATAAAGTGTCTGGGTACCATTATGGGCTCCTCACCTGTGAAAGCTGCAAG
Seq A exon
GTTTGCTCACACATTGCTACCTGAAAAATATAATGTCCAACACCAAAATAAACCAGTGGATTACTTCTTTTAAGCTAAATTTAGGCTCCTTTTTTAAAGACTCAACTAAAAATGAGGGAGAAAGAGAGAGTCTTAGGGAGATGATTCTTAGAAGTGTGTGTCTGATTTAGTTCAAAAGGCAAAGAAATTTATGCTGTTTAGAAAACTTTGCCAGTCTCATGGTTCTAAAATACTTTATTGTAGTAAAGTGATATAGCTGTAGAAAGACTTCCATTTCTAACAGTCCTAAATATTGATTTTGCTTGACTTATATATATTTAAAGCATCGTTGTTCTTGAAAGGGAATATGACAAACTATTTCCCAAATACATTTTAACTTCAGAGTATTTCTGTGCTATAAGTCTAAACATTCTTTATCCACAGACATAAAAGCCTAAATTCCCAACTGTGTGATTTCATCTTGATTTATTCCAAAATAATTTTAAGGATTTTTTGAAATTTATATCATAAAGACCAAGAAATCAGATTTTAGTTTTTAATATAATAATTTTTATAAATATATGACCTATTTAAGTGCATGGATTTTAATATGTAAAATATGCTATATTGTTACCAAAAATATAAATTATACTTTAAGAATTTATCTCAGGACTTTTTAATACATTCCCAGTAAATTCAATATTCACTATTTTTCAAAGTTTTTTTTGTTTGTTTGTTTTTGTTTTTAAGTGGAAAACTCAGTACAATTACTTAAACCACCACCAGGAAAATCCCTCCATTCTCTATAACAAAGTAAGAATGTTTCTCTTTGTGGCAAGTGGGTTAAATATGAATACTATCCTGGTAAATCTCATATTATAAAGCTACACATTTTATTTTTGATTAATTCTTTTATATAAAATATAAGGAAAGCTCATACCCTGTGTGCTACAATTCAGCTATCTGTGATACATGCTTTTTCCTTCCATTAGTTTTGCCTTTTTAAGAACAGTTCCCATACTTGAATGTATTCCAGTGGAATTATGAGCATTTTCCCATTTTACTCTTTAAATCCTTTTGCTTTTAACTATCCAGTGTTGACATTTGTTAAAAAAAAAAAAAAATCTGAGGTGTTTTGCTATTCAGTTTTTTCCACTGGCATTTTGCAATGGTTTATCACTGAAATTATATCAGACTACTTAAAAACAATGCCAGGACTTCATGAGTACCTCTATCAGGAACATGTGGGATAATAGGAAAATAGATTAAAAAAAAATTTATCTATATAGAGTGTATTTTTTCTGACTGTTGGGATAAAATGGTGGGTAGCCAAATCTCCCCAGGATTTGACGTAATTCTTCAAGAATAAAACTGATGCCAGAAAAATCTCCACCATGGCCTGGCACAGTTTGGGAAGGTTGATGTTGCTGAAATGTAAAATAAACCACAGAACCACATAAGGGCTCAAATAGTGCAATGAGAGGATTTACTGGTGATTTTCTTAAAATGAAACAATGGAAAAGACGGGTGTTAGATTTATAATACGTCTCACTATTTTCTCTGTCTTATAG
Seq C2 exon
GGATTTTTTAAGCGAACAGTCCAAAATAATAAAAGGTACACATGTATAGAAAACCAGAACTGCCAAATTGACAAAACACAGAGAAAGCGTTGTCCTTACTGTCGTTTTCAAAAATGTCTAAGTGTTGGAATGAAGCTAGAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000116833-NR5A2:NM_003822:2
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0010513=zf-C4=PU(32.9=57.5)
A:
NA
C2:
PF0010513=zf-C4=PD(64.3=93.8)
Main Inclusion Isoform:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TGGTGAATTACTCCTATGATGAAGA
R:
CTTCTAGCTTCATTCCAACACTTAGA
Band lengths:
246-1796
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)