RnoINT0103003 @ rn6
Intron Retention
Gene
ENSRNOG00000005964 | Nr4a3
Description
nuclear receptor subfamily 4, group A, member 3 [Source:RGD Symbol;Acc:61882]
Coordinates
chr5:63804027-63807631:+
Coord C1 exon
chr5:63804027-63804226
Coord A exon
chr5:63804227-63807452
Coord C2 exon
chr5:63807453-63807631
Length
3226 bp
Sequences
Splice sites
5' ss Seq
CAGGTGGGT
5' ss Score
8.56
3' ss Seq
CCTCCTCTGCCCACCCCTAGGTC
3' ss Score
11.68
Exon sequences
Seq C1 exon
TACTGTCCCACCGACCAGGCCACTGCGGGCACAGACGCTGAGCACGTGCAGCAGTTCTACAACCTTCTGACGGCCTCCATCGACGTGTCCAGAAGCTGGGCAGAAAAGATCCCCGGATTCACTGATCTCCCCAAAGAAGATCAGACGTTACTTATAGAATCAGCCTTTTTGGAGCTGTTCGTTCTTAGACTTTCTATCAG
Seq A exon
GTGGGTCCTATTCTACCTTCTGTCAGTCTCCTCATTTATAACAGTGAGAAGTCTGTTCAAGAAGCAAAGATGAAATGCATTCAAACACTGAGTTGTGGGGAATGGAAAGCCCCAAGGTGAGGGGGTGCAGGGAGTAGGGGCAGGGCGCCGCTAGGACCCTGGGCTCTAGTCTGAGGTCTAGACACCTTGTAGGGCTCTGAGCAGAGCGTTGCCTCACTAGAAATCCAGTTCTGTATGATGCAAACCAGAGAGCATGGATCTGATAGTCCCTCACGTCCATGGCCCCAGGACCGTTCTCATGGTACAGAAGGTGTTTGTGGAAATACCGGGTTGGCCTGATGAGTTGCATATGGGCCTCTGGAAGCTCCACAGATGAGCGCTCGGCTCAAAAGATGTGGCTCACCCATGAGTGTTGAGTGCCAGCGAGCATGAGGAGGAGTGGATTCCTTTTATTTTTTTAATCTATTTTTATATACATTGGTATTTGTACACACGTGTATCTGTGTGAGGGTGTCAGATCCCCTGGAACTGGAGTTATAGACAATTGTGAACTGCCAGGTGGGTGCTGGGAATTGAATGAGGGTCCTTTGGAAGAACAGCCAGTGCTCTTAATCGCTGAGCCATCTCTCCAGCCCTGAGGAAGTGAATTCTATCTACCTGCCTATCTGTCTGTCTATCAATCATCTATTTATCTATTTATCTATCTATCTATCTCTCATCTGCCATATATATATATATATATATGGATCAATAGGTCTCATATATATATGTATATATATATATATATATATATATATATATATATATATGGATCAATAGGTCTCACTAGGTCATTTAGACTTGAAGACTCACAGTGCCCTTGAGCTTGGAATCTTCCCTGTTCCAACCTCCTGAGTGCTGGGGCCCAGAGGTGCACTGCCATGCCCAAGAGAAAGTGAGTTTTCAAATAGCTTGAACCCAGACCTAAGCTCCTCTCCACACATGTCCCTTTTTGAAGATAAAAAAAATTTTTATTCACCCGGGGCATATTTAACTCCATCTTCCTTGCTTCATTTCAACTACATATCAGAAATAGGCCTTTCCTTCACCGGGCATTATAAGAGAAACTGTCATTTCCCTCCTTCTCTCTTCTCTAGCACCTGGTCCCATTTCATATTGTGACACCAGAAACTCCTACATAAAATGTAGCTCCTATGCTCCTCCCCTCCCCCCAACCCCCAACCCCGCCCACTCTGACCTAGCAGCCTATAGAGTATAATACTGGAAACTGCATTGTAACTCCTACTCCCATGATCCTGAAACCGGAGGTTAGAAGTCCATGTTCAAACTCGGTGGAAACATTCTGTCCATCTGCCCCCTGTGAAGAAGGATCTGGCGGAGAGATGGGGGCTTGTGGCTAGAGTGTCTGGTTTTAGCTTAATTCCAAGCCAGTGCAGTGCACGTGAGAGTTGGTAGTGAGGTGCCTGCCACCTTAGGCGAGTAGCAAAGGACTCAGCCAAGGATAAACTCCGTGCAGGTGGGCACCCCAGCTCACCAAGCTCCAGCACCTATGTCCAGCAGCTTCTCATCCTTGGTGCTCAGTAAGGACCGGCTGAGTGAAGGGGTAAATAGAGCTATTCGTCGGGAAGCGCAGGCACTGGCTTGCGGATGCAGTCCTCCTAGAGAGGGAAACATGAAGCCAGATTGCTGAAAGTTAAGGGACAGCCAAGATTAAAGTAAGGATCCCACAAAATGGAGACTTGGTTACACCTCGTGCCCTCTGAACCATTCTGTGCTAGACCCTGTGCACCGGCTTTCAAAGGCCTCTGCAACCTTAGGAAACCATGATTAAAATCCTGTTTCACAGATAAGAGAAAGGAAGTCCAGAGAGATGAAAGGAGTGTCCAAGGTTACACTGCTAAGCCGTCTTGTCGGATGGAGGTTCCAGGGCTCCTTTTATAAGAAGGGGATGGTTACAGATACATCGGCAGATTTCCACAGCCCTCTATAGCTCCCTAGTTTAAGTCCAAGGAGACAATGCATTCCGCCCCCTTCGGCTAGGCTCTGAGATTGGCACTTTGAGTTTACATAATGGAATTACAGAGTCTAGCCTCAAGCCTTATCAGCTTCTGGCATTTAAGGAAATAAGGGAGCAGCCTTGAACTGCAAGCCCCAAGGGGGAAATCTCCCATTTGCCGCAGAGAGGGGGGGGCCATTGTGTGACTTTACTTCAGGAGACCTCCCAACAAAGGTCTATTCACCCCAGAGAGGGGACCAACAATAGGCCAAAGAAATGATTTTATCCAAGTTCAGGATGACGAACCAGTATATTTACTGGGCTAACTATTGGGAACACATATGAGGGTCTGCTTACAGTCGTGTGGGTGTGTCCCTCCCAAAGATGTATCACCAAGAACTCAGACCTACATAACGTGAATAATAACCTCCCAAAAGTCACAGAGATGGATCCCCTGCTTCAGCCGGTTTCCCGCCTCCCACAGACTTCTGCACTGCCCTTGGCTGCATGGAACTGGGTGGGGCAGCAGTATGCACTTCTGGGTGTGGAAAAGCAGGGGAGAGTCAATGGCTGTAACATCTGCTGAGGGTCTCATGTTCTGCTCCTCACTTCTGTGAGGGAACCTCGTAGGCCTGCAGTTGTGTCGAAAACCACAGCTATGCTGATTTCAACAGAGTAACAGATATGAATTAGCCAGAAGTCATGTGCTAGGCATTCCCCAGACCAGTGGTTCTCAACCTTCCTAATCCTGGGACCCCCTTAATACAGTTCCTCATGGTGCGGTGCGTTGACACCCCCAGCCATAAAATTATTCTTGTAACTGTATTTTTGCTACTCTTATGAATTATTATGTAAATATTTGATATGCAGATGGTCTTAGGTGACCTCTGTGGACACCTACCCCCAAAGGGGTCACAACCCACAGGTTGAGAATCACTGGACTAGATGTTCTCTGAGGATCTGCCTCTCCACATTCCCTCCCAGACAAGCCATTAGCCTATGCTCGCCCTAGGCACACTCCATGTCTTGGCCTATGTTCCCTGAAGACGTTAGCACAGACAGACGGTACAGGCCGTCCAATCCCAGGAACACACCTTTGTTCATGGCAGTGCTACACAGTTTCCAGTGCTGCCCCGTGTGATGTCGGTACCCGTGTATTAGGACAATACCATGTTAGCCAGACTGAGAAGACCTATTTAACGTGTATCTCCCTCCTCTGCCCACCCCTAG
Seq C2 exon
GTCAAACACTGCTGAAGATAAGTTTGTGTTCTGCAATGGACTTGTCCTGCACCGACTTCAGTGCCTTCGCGGATTTGGGGAGTGGCTCGACTCCATTAAAGACTTTTCTTTAAATTTGCAGAGCCTGAACCTTGATATCCAAGCCTTAGCCTGCCTGTCAGCACTGAGTATGATCACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000005964:ENSRNOT00000008302:6
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=0.000
Domain overlap (PFAM):
C1:
PF0010425=Hormone_recep=PU(33.0=92.5)
A:
NA
C2:
PF0010425=Hormone_recep=FE(31.9=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
No suggested primer sequences
R:
No suggested primer sequences
Band lengths:
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]