RnoINT0102999 @ rn6
Intron Retention
Gene
ENSRNOG00000005964 | Nr4a3
Description
nuclear receptor subfamily 4, group A, member 3 [Source:RGD Symbol;Acc:61882]
Coordinates
chr5:63785548-63788780:+
Coord C1 exon
chr5:63785548-63785727
Coord A exon
chr5:63785728-63787821
Coord C2 exon
chr5:63787822-63788780
Length
2094 bp
Sequences
Splice sites
5' ss Seq
CAGGTAGGT
5' ss Score
10.28
3' ss Seq
CCCTTTCTCTGTCCCTGTAGATA
3' ss Score
12.64
Exon sequences
Seq C1 exon
AGCCCACTGCGGGAGAGCGCAGCCCGACAAGCCCGGGCGCTGAGCCTGGACCCTCAACAGAGCGGGCCAGCACAGCGGCGGCGGCTGCTTCGCCTATCCCGACGTCCCCGCCTCCTACACTCTCAGCCTCCGCTGGAGAGACCCCCAGCCCCACCATTCAGCGCGCAAGATACCCTCCAG
Seq A exon
GTAGGTCCGAAGCCCTTATTCCTCCGGAGCAAGGGAAATGGGTGGAGAAACCAACAACCAGCGGGCAGTCTGGTCAACCTGCCCAGTACCAACATGTAGGGCTACTGACCCTACATTTCACAGCACAGGAGCTTCCTGGCACGAAGCTCCGCTGTATACCACACCCTGTTGCTACCAAGCAGAGCAGAGAGAGTACACGAAGCATTTCTCCAAAGTATGTTTCCTAAGAAGAAAAGCAAATACTCCAAGCGATCGGGATATGCTATGTTTTTAATGGCTTTCTTTTTGTCCTTTTATATCCAATATATTCATTTAAGAGATCACTTGGGGAGATAGGGAACCTTTTTATTGATCTAAAACCCAGATCATTTGTGGTGCAGGAGTTTGAGGTGATTGAGGCAGAGAAGTAAAGGTAAAGGGCCCGGATTTGGTTTACAGGCCTCTTTACAAATTTGGTAAAGGTATAAGAAGAGGCGGGCCTGGATAGGCACCAAAGATACACAGATACAGTCACTCTCCTGCTGGAGACTTCAGAAAGACAAAGAGCCAATAGGGAGAGGACAGAATAGCAGGTGATTCTGAGAGATTCTTAGAGATGCAAGAGGGGGAGGGATGTAAAGGCCACGCTGTGTCTTTTAAACAGTTTCCATTTCATCCTAAGAACTAGACACCAAGCTAAGTAATTCTTTAACTCCAAGCTAGCTCAGGAGGCCTCCCTTGAGAAGGCAGGCATGAACCGGCCACTCCTCAACACTGCTTCTTCCAACAGGCCCTCAGCACCTTTTTTCACGTCAAGATTTCATCCCATACACGCATGACTCAATCAGCTTTGGAAATGTGGGTAAGAGAAAGATGTGAAGGGAAATGTGAAGCACCCACTTTTCTGCTAATCACACCTTCACACCACACCCTCCAAGAAGACTGGAGGCACCTGGGTTTCCTTTGCCTCGGAAAAACCAACCACCAGAAACTCCCCATGCTACCACTTTGACTTAGCCATAAAAAAAAAAAAAAGAAAAGGAAAATTATTAGAAAAGTCATTCACAGAGCCAGTAACTCTCGGGGCCTTCACACCTTCCTCCACCTCTGTGAATATAGCAAGCACCTCTCTACCAGCTGCTTTGGGGGTCCAGCCTAGGCAAACTGGCAGAGAGACTGTGTCTCTGTTTTGAAATTGCTTTCATGAGAAAATACCTAGACCAATGTGCCTGTTAGAAGAGCTGTGAGCTGTTGTTATAAAACCGCTCTGATCCTACTGGGTTAGATTATCCTATTAGTCAGAATTGGGAAGGGTATACATATATGCATCCGCACACAGCATATAGGAGAGAGCAGGTTTGGTGGGTGTGCTGTTACAGCTGAGCTTTTTCTTTGCAGATGGCACAGACTCCCCCGGTCCATTTCCTGGGCCTACATGCCCACCTCACCACTTAAGCCGGCTGAAGTCATCAGTAGGGGTCCAGTTTGTGCAGGCTGCTAATCCTGTTTGGAGGAGTGGGTGGGAAGCAGCAACCACAACTTGTGTGGGCAGCCTTAGTTGGCACTCATAAAATGTTAGCATGCCACTGCCTTCCTTGTCCCACAAGGGACCTCTCCCCCCACCAATAACTCACAGGTTTACAAATCAACCTATGTATATCTTGGGGGATCAATGGCCTCCTCTTCAAATTAATTAACAAGTTATTTCCTTCCTTTCCCCTTGGCCTTCCCTATGGCTAAGGAGACAACTCCAATTGTTTTTGGGAGAGTGTCGTCGTTGTTGTTGCTGTTGTTGTTGTTGTTTAGGAGTTAAACTAATTTTAAAAATGGGCTTATGAGAGAAAGCATCTATATCAAAGTTTAATGAACAGAGCAAGGGAGAGAAGATGGGTGTAGCCACCCCAGGGAGTCCATTTTATTGCCGGTGGGGCCCCTTTGTCAGTCAGGGTCTCAGCTGTCTTCTCAGGGAGGAAGAAAGGAGGCTAGGGGCATTCAGCCTTCGCCAGCAGGTGGGAGAGGATGCCACTCTGTTTCCTGATTCTGGAGAGCAGTGGATCCACGTGGTGACCGATGGAGTGTCAACTGGCTTCTGAGCCCCTTTCTCTGTCCCTGTAG
Seq C2 exon
ATATGCCCTGCGTGCAAGCCCAATATAGCCCTTCGCCTCCGGGGTCCACTTATGCCACGCAGACTTATGGCTCGGAATACACCACAGAAATCATGAACCCCGACTATGCCAAGCTGACCATGGACCTCGGTAGCACGGGGATCATGGCCACGGCCACGACGTCCCTGCCCAGCTTCAGTACCTTCATGGAGGGCTACCCCAGCAGCTGCGAACTCAAGCCCTCCTGCCTGTACCAAATGCCGCCTTCTGGGCCTCGGCCTTTGATCAAGATGGAAGAGGGTCGCGAGCATGGCTACCACCACCACCACCACCATCACCATCATCATCACCACCACCACCAGCAGCAGCAGCCGTCCATTCCTCCTCCCTCTGGCCCCGAGGACGAGGTACTGCCCAGCACCTCCATGTACTTCAAGCAGTCTCCGCCGTCTACGCCGACCACTCCAGGCTTCCCCCCGCAGGCGGGGGCGCTGTGGGACGACGAGCTGCCCTCTGCGCCTGGCTGCATCGCTCCGGGACCGCTGCTGGACCCGCAGATGAAGGCAGTGCCCCCAATGGCCGCTGCTGCGCGCTTCCCGATCTTCTTCAAGCCCTCACCGCCACACCCTCCCGCGCCCAGCCCAGCCGGCGGCCACCACCTGGGCTATGACCCCACGGCCGCAGCTGCGCTCAGTCTACCCCTGGGAGCCGCGGCCGCCGCGGGCAGCCAAGCTGCTGCGCTCGAGGGCCATCCGTACGGGCTCCCGCTGGCCAAGAGGACGGCCACGTTGACCTTCCCTCCGCTGGGCCTCACAGCGTCCCCTACCGCGTCCAGCCTGCTGGGAGAGAGCCCCAGCCTACCATCGCCACCCAATAGGAGCTCATCATCCGGCGAGGGCACGTGTGCTGTGTGCGGGGACAATGCTGCCTGCCAGCACTACGGAGTCCGCACCTGCGAGGGCTGCAAGGGCTTCTTCAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000005964:ENSRNOT00000008302:2
Average complexity
IR
Mappability confidence:
NA
Protein Impact
5' UTR
No structure available
Features
Disorder rate (Iupred):
C1=NA A=NA C2=0.555
Domain overlap (PFAM):
C1:
NA
A:
NA
C2:
PF0253517=Zip=WD(100=34.8),PF0010513=zf-C4=PU(38.6=8.5)
Main Inclusion Isoform:
NA
Main Skipping Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Mouse
(mm9)
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:
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]