RnoINT0102995 @ rn6
Intron Retention
Gene
ENSRNOG00000005600 | Nr4a2
Description
nuclear receptor subfamily 4, group A, member 2 [Source:RGD Symbol;Acc:3202]
Coordinates
chr3:43113503-43114707:-
Coord C1 exon
chr3:43114544-43114707
Coord A exon
chr3:43113706-43114543
Coord C2 exon
chr3:43113503-43113705
Length
838 bp
Sequences
Splice sites
5' ss Seq
AGGGTAAGA
5' ss Score
9.21
3' ss Seq
TTTTTAAAATGAAATTCCAGTTC
3' ss Score
3.59
Exon sequences
Seq C1 exon
TGGTTCGCACGGACAGTTTAAAAGGCCGGAGAGGTCGTCTACCCTCAAAACCGAAGAGCCCACAGGATCCCTCTCCCCCCTCACCTCCGGTGAGTCTGATCAGTGCCCTCGTCAGAGCCCACGTCGACTCCAATCCGGCAATGACCAGCCTGGACTATTCCAGG
Seq A exon
GTAAGAAGCTTGTGGGGTAAGAATATCATGTGGACAAGCCAACAAACGAGCAAGACCCTCGCACTATACCCAGCTTTAGTACCCCCAGACTCAAGGGTAAAGGAGGCACACCGGAATATATACTTCACAACTTTGGGGAGGTTTTCAGGAGACAGAGAGACGGTGCACTTCAAAGTCTAGACCGAAAACACGCCAGAGGGGTTTCATCTTTGTGAACCATTATTGTCCGGCAGTCCCTCCAACTGCGGTCTGAAAGGCAAAACCTTAACCGTCCATGCCTAACCTTCCTTCCGACGTCTACTTACGTAGAAGTTACTAGAATACTCACCCATGACTTATCTGGGGCCAGGGAGTGAAAAGAGGGGTAGAAGGGATGGCAACGGGGCTCTCGGGGTCAGAGATCAAGTGGTGCAATTCTTCTTTTACTCCAGCTGTGAGAAATGTGCAGGCTTTGGTTGGAGGGAGTGTGGGCAAACCTAGTAGCGACTGCAAGATTATTAAGCTCTGCAAAGGGCGCCTCCGCTCAAGACCCACTCTGGGATTAGCATGAATACTACCGTGTCAATTGTTTTGTGGAGATAAGACTGAACGTTTCCCAGGGCTGGATGGCACTGTATTTAGTCTGTATGGAAATGGTAATTTACATATTTAAAGCAGCGACCTCATAGCACCGTCCCTAATTGAATTAATTGCCCCGGAACATCTAATTTCCTTACTGGTCAGAGAGAGGTTTAATTGTTATAAAAACCTGGCTCCCCTACTAGAAACGGGGTTAGCAATTTCACGGGTTATATATTTTAGAGAACCTCATTAAGTGCTTTTTAAAATGAAATTCCAG
Seq C2 exon
TTCCAGGCAAACCCTGACTATCAGATGAGTGGAGATGATACTCAACATATCCAGCAGTTCTACGATCTCCTGACTGGCTCTATGGAGATCATCAGAGGGTGGGCAGAGAAGATTCCTGGCTTTGCTGACCTGCCCAAAGCCGATCAGGACCTGCTTTTTGAATCAGCTTTCTTAGAATTATTTGTTCTACGCTTAGCATACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000005600:ENSRNOT00000041394:5
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.473 A=NA C2=0.022
Domain overlap (PFAM):
C1:
PF0010425=Hormone_recep=PU(0.5=1.8)
A:
NA
C2:
PF0010425=Hormone_recep=FE(33.8=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CGGACAGTTTAAAAGGCCGGA
R:
CTGTATGCTAAGCGTAGAACAAAT
Band lengths:
358-1196
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]