RnoINT0102994 @ rn6
Intron Retention
Gene
ENSRNOG00000005600 | Nr4a2
Description
nuclear receptor subfamily 4, group A, member 2 [Source:RGD Symbol;Acc:3202]
Coordinates
chr3:43114544-43115199:-
Coord C1 exon
chr3:43115070-43115199
Coord A exon
chr3:43114708-43115069
Coord C2 exon
chr3:43114544-43114707
Length
362 bp
Sequences
Splice sites
5' ss Seq
AAGGTAGGT
5' ss Score
10.29
3' ss Seq
CTTGAATAATTCCTTTACAGTGG
3' ss Score
4.3
Exon sequences
Seq C1 exon
CGCACGGTGCAAAAAAACGCGAAATATGTGTGTTTAGCAAATAAAAATTGCCCAGTGGATAAGCGCCGCCGAAATCGTTGTCAGTACTGTCGGTTTCAGAAGTGCCTGGCTGTTGGGATGGTTAAAGAAG
Seq A exon
GTAGGTCCGGGCAAGCTGTTGACCTCCCATTCCTCGCCCTTGAAAGACCACCCCAGCTGCTTGTGGACTCTTGTCCCTGCCTCACTCCCTAGCCCCCTGACTCCAGGATTCCTCTGTTAAATTCCCTCCTCTAAAGAAAGCCACCCGACGGCCCTCCTTGTCTCTAAGTATAGGACCTAGTTGGAGGAAGGTCTAAAATAACCCGCGGTTTATTAATGCTTTTCGTCAGTAGAGTCTTTACAAGCAGAGGGGCCCTGGACCACCAGGTCGGGCTTCCACTGCTTCCTCCCGGGAGGAGCGGGTGAAACAGCCGAGTCTGGGCTCAAGGGAACAGCGTTAACCCTTGAATAATTCCTTTACAG
Seq C2 exon
TGGTTCGCACGGACAGTTTAAAAGGCCGGAGAGGTCGTCTACCCTCAAAACCGAAGAGCCCACAGGATCCCTCTCCCCCCTCACCTCCGGTGAGTCTGATCAGTGCCCTCGTCAGAGCCCACGTCGACTCCAATCCGGCAATGACCAGCCTGGACTATTCCAGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000005600:ENSRNOT00000041394:4
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.473
Domain overlap (PFAM):
C1:
PF0010513=zf-C4=PD(58.6=93.2)
A:
NA
C2:
PF0010425=Hormone_recep=PU(0.5=1.8)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AAAACGCGAAATATGTGTGTTTAGCA
R:
GGAATAGTCCAGGCTGGTCAT
Band lengths:
278-640
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]