RnoINT0102992 @ rn6
Intron Retention
Gene
ENSRNOG00000005600 | Nr4a2
Description
nuclear receptor subfamily 4, group A, member 2 [Source:RGD Symbol;Acc:3202]
Coordinates
chr3:43115954-43117421:-
Coord C1 exon
chr3:43117298-43117421
Coord A exon
chr3:43116820-43117297
Coord C2 exon
chr3:43115954-43116819
Length
478 bp
Sequences
Splice sites
5' ss Seq
AAGGTTAGT
5' ss Score
8.54
3' ss Seq
TCACCCTGTTTCATTTCCAGCCA
3' ss Score
9.82
Exon sequences
Seq C1 exon
GGAGATCTGACGGGCTGGATCCCCAAATTGCTTTTTAAAAAATATCTTGGAAACTTTGTCCTTTGCTGAATTACGACACTGTCCACCTTTAATTTCCTCGAAAACTCCAATCACTCGGCTGAAG
Seq A exon
GTTAGTGAGCTTTTTCTTTCATTACCTTTCCCGAGTTCCCCATATATCCGGGAGGGGGGGAACCCAGGGCAACAGAATCTTTTCAGGCCAACCCTGTGCCTTATGGTCACAGAGAACAACTTTCTCATTGTGCAATTCAACTTCATTTCTAGATCATGGGTTCTAGAAATCCTTGTCGACCCTGAGCTTCAACGAAGACGCTCACCAGAGTGGGAGTGTGTGTTGGGAGGGGGTGGAGGGGGTGGCTTTTGGAATATCCGGGAGTGTAGACCCTAAACAGCTTCCCAGCTCTGGGTCCAGGAATCAGCCCTTTCTTTCCTTCATCGCTGTTCAACCTCTTTTGCCCTAACCCTTGCACCCCTATCCCCCCATTCCCCCTGACACCGCGAGCTGCCGGTGTAGCTCCAGGTGTACCCGAGGCCGGAAGAAAGTGTTCAGTTGACCAGGCTGAGTGTATATCACCCTGTTTCATTTCCAG
Seq C2 exon
CCATGCCTTGTGTTCAGGCGCAGTATGGGTCCTCGCCTCAAGGAGCCAGCCCCGCTTCTCAGAGCTACAGTTACCACTCTTCGGGAGAATACAGCTCCGATTTCTTAACTCCAGAGTTTGTCAAGTTTAGCATGGACCTCACCAACACTGAAATTACTGCCACCACTTCTCTCCCCAGCTTCAGTACCTTTATGGACAACTACAGCACAGGCTACGACGTCAAGCCACCTTGCTTGTACCAAATGCCCCTGTCCGGACAGCAGTCCTCCATTAAGGTAGAAGACATTCAGATGCACAACTACCAGCAACACAGCCACCTGCCCCCTCAGTCCGAGGAGATGATGCCACACAGCGGGTCGGTTTACTACAAGCCCTCTTCGCCCCCGACACCCAGCACCCCGGGCTTCCAGGTGCAGCATAGCCCGATGTGGGACGATCCGGGCTCCCTTCACAACTTCCACCAGAACTACGTGGCCACTACGCATATGATCGAGCAGAGGAAGACACCTGTCTCCCGCCTTTCACTCTTCTCCTTTAAGCAGTCGCCCCCGGGCACTCCTGTGTCTAGCTGCCAGATGCGCTTTGACGGGCCTCTGCACGTCCCCATGAACCCGGAGCCCGCGGGCAGCCACCACGTAGTGGATGGGCAGACCTTCGCCGTGCCCAATCCCATTCGCAAGCCGGCATCCATGGGCTTCCCGGGCCTGCAGATCGGCCACGCGTCGCAGTTGCTTGACACGCAGGTGCCCTCGCCGCCGTCCCGGGGCTCTCCCTCCAATGAGGGTCTGTGCGCTGTTTGCGGTGACAACGCGGCCTGTCAGCATTACGGTGTTCGCACTTGTGAGGGCTGCAAAGGTTTCTTTAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000005600:ENSRNOT00000041394:2
Average complexity
IR
Mappability confidence:
NA
Protein Impact
5' UTR
No structure available
Features
Disorder rate (Iupred):
C1=NA A=NA C2=0.514
Domain overlap (PFAM):
C1:
NA
A:
NA
C2:
PF0010513=zf-C4=PU(38.6=9.4)
Main Inclusion Isoform:
NA
Main Skipping Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GGCTGGATCCCCAAATTGCTT
R:
CAAGGTGGCTTGACGTCGTAG
Band lengths:
344-822
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]