RnoINT0102991 @ rn6
Intron Retention
Gene
ENSRNOG00000005600 | Nr4a2
Description
nuclear receptor subfamily 4, group A, member 2 [Source:RGD Symbol;Acc:3202]
Coordinates
chr3:43117298-43119159:-
Coord C1 exon
chr3:43119065-43119159
Coord A exon
chr3:43117422-43119064
Coord C2 exon
chr3:43117298-43117421
Length
1643 bp
Sequences
Splice sites
5' ss Seq
GAAGTGAGT
5' ss Score
7.97
3' ss Seq
TTCCTCTGTCTGTATTTCAGGGA
3' ss Score
11.32
Exon sequences
Seq C1 exon
GCCCCGCTCCCGCAGCGCTCCAGCGGACCCCGGCTCCTCTGCTCCCGGAGGGAACTGCACTTCGGCGGAGTTGAATGAATGAAGAGAGCGGAGAA
Seq A exon
GTGAGTAGAAGCGGCGGGATCACCGGCGGTCACGCGTCCTCCGGGTCTCCGCGTACCCGGAACGGGTTCTCTGCAAGTGGGCGCTGGAGCCCCGGAGCGCGAAGGGGCTTGGGGTGCGGAGGGGGGGTGGCGAGTGGGCGCGCGCAGCTCCGCCGAGCCTTTGCTGGAACTCCGGTGGTAGCGTAAAGCGGGGGGAGTTGGCTGCCGGCAGAGGTTTCCAGGCTTCTCATTGGTGGATGTGGCAGGGGGGACTCCCACAGTTTTAGGGGAAGCGGACTTGCCTGCGGAGATGTGCTCAAAGTTTGCTCTTGGTGTGAAATTGATTGTGGCTTGAGTAGGCTCCATCTCGTGAACATGTGGGAAACAGTCCGGGAGAGAAAGTTTACGTGTTGCTTGGGAACAGTGTCGCTCAGCTCGCCCGCTTGCGGAGGTTTCCCGGATATCGTCGAGCAAGGGTAGTGTCGGTAGAGGGTCCCGTTGCGAAGTTGCCTGAAATTTCTTCTTTTGGTATATGCTGTCCTTGGGTAGTGTGTCAGTGTGTGCGTGAGGTAAAGAATACAGTTATGAAACTGTGACACAGCCTCGGGTTAATATCCAGCACAGACATATTTTCAAGGGCGGCGGCGGATGGGGTTGGTGGGCTGGGGGATAAGGCAAGAGTCCTCTGGTTTTTCTTGTTAACCTTCTCCACTCCGTAAAGCAAGCAAGATTATGGAAGAAGGGAGAGGGATCAGAAGGAGAGGGTGTTTGGGTTTCTTTTCTTTATTTTATGAACAAGATCGTCCATGCTCTAGAATGCCTTGCAAGTGGGGACATCTGAAAAGAGCTAGAACATAAGAATGCCTTGTCCCAGCAAGTAGGCAGCCGGTGGAAAGCATTGTGGAGAAGGTGCTAAGCTTGCTGTGCTGAGAAGTGGTTCTAACGTTGGTGCCAATATCATATAAATAATATTTCCTTCCCTCTGCAGTTGACCCAAGATACTTCTGGTAAAGTAGAGGTCTCTCTCATCACCTCTGAGCCATGAAAAGTGTTGAAAATCCAGTTCTCTGGAGGAACACCAATTCACTTGCCCCTCAAGCCCCATTTGATTTTGCTGGAACAAAATCAATTACAAAAGCCACCCTCGCACCCAAATTAGCTTCTTCGTTGTCCAGGACTTGCTAACGTTTTTCTAAGGATGGGATCTCTATTGTTTTTTTCCCCACGGTGTACTCTTGAGTTCTACTAACTTTCTTTCTCCCTCTAAGAGAAAAGTCCATTTGACTACAAGAAAATTATTAAGAGGCGGCTTTGATGCTGTGTTTTCTCTTTATCCCAGACTTCTTAGGTTTGAAATAAAGTAAAATGACAAGGGCCTTTCCATCTATATCAAAGAAGGCCAATTCATTATATTGTCTAGTATCCAGTAGACTCCTGGGATAACTTCCCCACAGGATGCTTTCTCTGCAGGGAAACGGGGAGTTGAGTGGCATTCTCTGCTGCTTAGCCACCGCTATCCCTGCACATTCATTTTAAGCTGCTCTTTGGTATAGTCTTGACACTCTCTTCCAAGGAAAGCCCTGAAGGGACTGCTGAGTGAGTCCGCATCTGTCCAGCCAAGTCTCGGTGGGAACATCCTGAAACTTCCTCTGTCTGTATTTCAG
Seq C2 exon
GGAGATCTGACGGGCTGGATCCCCAAATTGCTTTTTAAAAAATATCTTGGAAACTTTGTCCTTTGCTGAATTACGACACTGTCCACCTTTAATTTCCTCGAAAACTCCAATCACTCGGCTGAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000005600:ENSRNOT00000041394:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
5' UTR
No structure available
Features
Disorder rate (Iupred):
C1=NA A=NA C2=NA
Domain overlap (PFAM):
C1:
NA
A:
NA
C2:
NA
Main Inclusion Isoform:
NA
Main Skipping Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GCTCCTCTGCTCCCGGAG
R:
CTTCAGCCGAGTGATTGGAGT
Band lengths:
187-1830
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]