RnoINT0102997 @ rn6
Intron Retention
Gene
ENSRNOG00000005600 | Nr4a2
Description
nuclear receptor subfamily 4, group A, member 2 [Source:RGD Symbol;Acc:3202]
Coordinates
chr3:43111240-43113180:-
Coord C1 exon
chr3:43113002-43113180
Coord A exon
chr3:43112854-43113001
Coord C2 exon
chr3:43111240-43112853
Length
148 bp
Sequences
Splice sites
5' ss Seq
CAGGTCAGT
5' ss Score
8.94
3' ss Seq
TCTGATTGCATTTTCTGCAGAGA
3' ss Score
7.59
Exon sequences
Seq C1 exon
GTCCAACCCAGTGGAGGGTAAACTCATCTTTTGCAATGGGGTGGTCTTGCACAGGTTGCAATGCGTGCGTGGCTTTGGGGAATGGATTGATTCCATTGTTGAATTCTCCTCCAACTTGCAGAATATGAACATCGACATTTCTGCCTTCTCCTGCATTGCTGCCCTGGCTATGGTCACAG
Seq A exon
GTCAGTACTGCTGGTGCAGGGTACTTCCCCTTTGGAACTTCCTCTGGTGGGACCGGTCATGGCTTTCCCTAATCACAGAGTCTCTCTGGATTCTGACAGCTGACTAACTCCCTGTGCATTCTTTTGTTTCTGATTGCATTTTCTGCAG
Seq C2 exon
AGAGACACGGGCTCAAGGAACCCAAGAGAGTGGAAGAGCTACAAAACAAAATTGTAAATTGTCTTAAAGACCATGTGACTTTCAATAATGGGGGATTGAACCGACCCAACTACCTGTCCAAACTGTTGGGGAAGCTCCCAGAACTTCGCACCCTTTGCACACAGGGGCTCCAGCGCATTTTCTACCTGAAATTGGAAGACTTGGTACCACCACCAGCAATAATTGACAAACTTTTCCTGGACACCTTACCTTTCTAAGACTTTCTCCCATGCACGTCAAAGAACTGGAAAGAAAAAAAAAATCCAGAGGGGGCTGGTCAAGATGGGTAGAGAGCTGGCTGAAGTGTCCGGTTCATGTCTCCCTTCTGTAGACCCCTAGCCCTCACCCCTAAAGTAAACAAACAAACAAGCAAACAAACAAACACAAATTAAAAACTGTTGCTATTTCCTAACCTGCAGGCAGAACGTGAAAGGGCATTTTGGCTCCGGGGCATCCTGGATTTAGAAAACGGACAACATACACAGTACAGTGGTATAAACTTTTTTATTATCAGTTCAAAATCAGTTTATTGTTCAGAAGGAAGATTGCAAATGTATGATGGGAAATGTTTGGCCATGCTTGCTTGTTGCAGTTAAGACAAATGTAAGGCAAATGTAACACACACACACACACACACACACACACACACACACACACACCTCTTAATGGGACCCTCATATTTTGCCCTTTAACAAGACTTCAAAGTTTTCTGCTGTAAAGAAAGCTGTAATATATAGTAAAACTAAATGTTGCGTGGGTGGCATGAATTGAAGGCAGAGGCTTGTAAATTTTATCCAATGCAGTTTGGCTTTTTAAATTATTTTGTGCCTATTTATGAATAAATATTACAAATTCTAAAAAGTAAGTGTGTTTGCAAAAAAATAAAAAAAGAAAATAACTCCATAAAAAGGGAACAAGCATGTGACTCTAGGTTGAAGATGTTATAGGCACTTGCTACTTCAGTAATGTCTATATTATATAAATAGTATTTCAGACACTATGTAGTCTGCTAGATTTTATAAAGATTGGTAGTTATCTGAGCTTCAACATTTTCTCAATTGTATAATAGGTGGGCACAAGTATCAATACATTGGAAAATCCTGACAAAAGGGACACATAGTGTTTGTAACACCGTCCAACATTCCTTGTTTGTAAGTGTTGTATGTACCGTTGATGTTGATAAAAGAAAGTTTATATCTTGATTATTTTGTTGTCTAAAGCTAATCAAAACTTGCATGCAACAGCTTTTGACTGTTTCCAGAGTGCTTATAATATACATAACTCCCTGGAAATTACTGAGCACTTTGAATTTTTTTTGTTTTTTTTTATGTCTAAAATTGTCAGTTAATATATTATTTTATGTTTGAGTAAGAATTTTAATATTGCCATATTCTGTAGTATTTTCTTTGTATATTTCTAGTATGGCACATGAGATGAGTCACTGCCTTTTTTTCTATGGTGTACGACAGTTAGAGATGCTGATTTTTTTTTCTGATAAATTCTTTCTTTAAGAAAGACAATTTTAATGTTTACAACAATAAACCACGTAAATGAACAGAATTTTGTCTTATTTCT
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000005600:ENSRNOT00000041394:7
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.058
Domain overlap (PFAM):
C1:
PF0010425=Hormone_recep=PD(16.5=75.0)
A:
NA
C2:
PF0010425=Hormone_recep=PD(34.3=79.1)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GGGTGGTCTTGCACAGGTTG
R:
ACAGGTAGTTGGGTCGGTTCA
Band lengths:
258-406
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]