RnoINT0102996 @ rn6
Intron Retention
Gene
ENSRNOG00000005600 | Nr4a2
Description
nuclear receptor subfamily 4, group A, member 2 [Source:RGD Symbol;Acc:3202]
Coordinates
chr3:43113002-43113705:-
Coord C1 exon
chr3:43113503-43113705
Coord A exon
chr3:43113181-43113502
Coord C2 exon
chr3:43113002-43113180
Length
322 bp
Sequences
Splice sites
5' ss Seq
CAGGTAATG
5' ss Score
9.43
3' ss Seq
CTCTTTGGTATTAATTGCAGGTC
3' ss Score
8.65
Exon sequences
Seq C1 exon
TTCCAGGCAAACCCTGACTATCAGATGAGTGGAGATGATACTCAACATATCCAGCAGTTCTACGATCTCCTGACTGGCTCTATGGAGATCATCAGAGGGTGGGCAGAGAAGATTCCTGGCTTTGCTGACCTGCCCAAAGCCGATCAGGACCTGCTTTTTGAATCAGCTTTCTTAGAATTATTTGTTCTACGCTTAGCATACAG
Seq A exon
GTAATGAGGGGGTCCTGGGGGAGGGATCAGAAGTAAAGAAAAGGGAGAAAGAAGGGTTGGGGTGGGGCGCAAGATAAAAACAAAACGAAGGTGAAGAAGGGAAAGAGTGGGACCAGAGCCTTGGGTGGACAAGTGGAGGTGGGGTAGGAGAGTCCTTGATTGTTATGAAATTAAACCCTTTCAAGGTCCACTGGTCGACATTTTATTAACTCTTCAGTAATTAGGTGCCTCTTAAATCCCTCATTTATTGCTCTTCAAGTAATTAGTTGTTTAGCTTCTCTCTCTCTCTTTTTCTCCCCTCTCTCTTTGGTATTAATTGCAG
Seq C2 exon
GTCCAACCCAGTGGAGGGTAAACTCATCTTTTGCAATGGGGTGGTCTTGCACAGGTTGCAATGCGTGCGTGGCTTTGGGGAATGGATTGATTCCATTGTTGAATTCTCCTCCAACTTGCAGAATATGAACATCGACATTTCTGCCTTCTCCTGCATTGCTGCCCTGGCTATGGTCACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000005600:ENSRNOT00000041394:6
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.022 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0010425=Hormone_recep=FE(33.8=100)
A:
NA
C2:
PF0010425=Hormone_recep=PD(16.5=75.0)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AGGCAAACCCTGACTATCAGA
R:
GCAATGCAGGAGAAGGCAGAA
Band lengths:
358-680
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]