RnoINT0103000 @ rn6
Intron Retention
Gene
ENSRNOG00000005964 | Nr4a3
Description
nuclear receptor subfamily 4, group A, member 3 [Source:RGD Symbol;Acc:61882]
Coordinates
chr5:63787822-63792636:+
Coord C1 exon
chr5:63787822-63788780
Coord A exon
chr5:63788781-63792506
Coord C2 exon
chr5:63792507-63792636
Length
3726 bp
Sequences
Splice sites
5' ss Seq
AAGGTGAGA
5' ss Score
8.68
3' ss Seq
TCTGTGTTATGTCTTCTCAGAGA
3' ss Score
8.93
Exon sequences
Seq C1 exon
ATATGCCCTGCGTGCAAGCCCAATATAGCCCTTCGCCTCCGGGGTCCACTTATGCCACGCAGACTTATGGCTCGGAATACACCACAGAAATCATGAACCCCGACTATGCCAAGCTGACCATGGACCTCGGTAGCACGGGGATCATGGCCACGGCCACGACGTCCCTGCCCAGCTTCAGTACCTTCATGGAGGGCTACCCCAGCAGCTGCGAACTCAAGCCCTCCTGCCTGTACCAAATGCCGCCTTCTGGGCCTCGGCCTTTGATCAAGATGGAAGAGGGTCGCGAGCATGGCTACCACCACCACCACCACCATCACCATCATCATCACCACCACCACCAGCAGCAGCAGCCGTCCATTCCTCCTCCCTCTGGCCCCGAGGACGAGGTACTGCCCAGCACCTCCATGTACTTCAAGCAGTCTCCGCCGTCTACGCCGACCACTCCAGGCTTCCCCCCGCAGGCGGGGGCGCTGTGGGACGACGAGCTGCCCTCTGCGCCTGGCTGCATCGCTCCGGGACCGCTGCTGGACCCGCAGATGAAGGCAGTGCCCCCAATGGCCGCTGCTGCGCGCTTCCCGATCTTCTTCAAGCCCTCACCGCCACACCCTCCCGCGCCCAGCCCAGCCGGCGGCCACCACCTGGGCTATGACCCCACGGCCGCAGCTGCGCTCAGTCTACCCCTGGGAGCCGCGGCCGCCGCGGGCAGCCAAGCTGCTGCGCTCGAGGGCCATCCGTACGGGCTCCCGCTGGCCAAGAGGACGGCCACGTTGACCTTCCCTCCGCTGGGCCTCACAGCGTCCCCTACCGCGTCCAGCCTGCTGGGAGAGAGCCCCAGCCTACCATCGCCACCCAATAGGAGCTCATCATCCGGCGAGGGCACGTGTGCTGTGTGCGGGGACAATGCTGCCTGCCAGCACTACGGAGTCCGCACCTGCGAGGGCTGCAAGGGCTTCTTCAAG
Seq A exon
GTGAGAGCATGCCTCCTCCAGGTACTTCCTCCACTCTGCAGTCAGACCCCTTGCTGAGGCGTCTACGTGAGTGTAGCTGAGTCCTTGCCCTTACCAATGTGAAAGCTATAATCCCACACACACCGTGCATTCCGATTCCTAGGCCTAGAGCTTCAGGCCCATCTTTCCCAGGGTTTTTAAACTCAAAGTTTCCGCATAAACTGTCCATGCATTTGAAGGGCCTTCACCAACCTCCAGACCTGACGTTGCTTTCTGAGGGTTTGGTTTTTTTTTTTTTTCCTGAATAGAGGTTTCTGCAAATTCTCAAAAGGATCTAAACTTCCACAATGCTCAAACATCACCACCATCATTACCCCTTCATTGTCTCCCCAGAGTGTGAGGAAATAGCACCTGCGTGGCAGGCCTGGGCATTTGTGTCTCAGTCTACACAGGATGAGCTGAGAGACTTAAGATTGGATTTTGGTCATTCACTGGCGCGGGTTTTTTTTCTTTTTAATTCAGTGTGCCTTGAAGCTAGATGATAATTATCGTTGTTTCTTAGAGGAGAAAATGGAGATTCAGAGAGGTCATTCCACTGCCACAGAACTCACACTCAGAGAGTGAGGTGGAGACAGGAGGTCAACTCATAATCCATGTGCTCCCAAGATGCTCTGGGGTGGCAGTATAGAGGGGGAAGGCCGTGTGGCTAGAAGCAGCTTGTGACAGCTTAGTCCTCAGAAGGGTAGAAGGTATCTCAGGCCCTGTCAACCCACCCTTTCCTCCAGTAATGCTTACCTCCCTGCATGTGTGCACACACAACACCCATGATGATCGTTCTCTTAGTGGAGAATTTTTCAGTGAGAGTGGCCTCCACATATTAGCAAAGAAACTGAACCCTGGAGAAGTATCCTGTGGTTAGTCTTATGCAACAATGTTGCTTGTATTTGGGATAGGAGACAGCTGGCTTCTCTTGACTCTGGAGTTCAATAGTCTTTCCCCCTCCCCCCATATGTGAGGGAGCAGTGCTGTTCTTCTGTTGTCACTGAGTCTCAGATGGTTCCAGACATTTCTGTGTCATTCTCTTTACACCCTAACCTACTGATAGATACTTCAGGCACAAACAGAAACATACAAATGACATAGGTGAAGTGGGATGCTGATTGGGTAACAAGGATTTGGGAGGCAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAGAGTATATATTTAGGAGCCAGAATCAGGGCTGGAAGATTCAAATAAAATTCCTAACTTGTCACCTATCAGTTATGACATTGGAGATAGCCCTTCTTTCTAGATCTTAGTTCCCCGACCAGTGGATCAAACACAAAGAAAGGCCATACTAAATTAGATATTATTTCATCTTTAAGACTTCCTAGCCTTTAAGTCACAAAACGCTAAGTACTGAATGAAGACTCCGTATTTATGACCGGCACATGTTTGTGGTTAGACATACAAGCCAACAGGCATCTGGTTGTCACATGACAATGGTTATCACATCACTCACTGAATTCTCCATGTGCATGAAAGGATGCTTGGGTAAGGATGTTGCCATGTTAGAGGCCCCCACGGATAAACACGTTTGTGATGTTTTAAGGGCAGAACTTCCTTCTAATAAGCCACTTGTTTTGCTTCATAAGCCTTTGTCTCTTGCCCTGAGTGCTGGGGGCTGAATCCAGGGCTTTGTGATTGCCAGGCCTGAGCTAGTCTCCAACCCTGGGTTAGCCTCCCCCTTCTCTTCCTTTCTCCCCCCTCTCCCTGTTACTCGAAGTTTCCCATAGCCACTACCACATACCTGCGTTCCCTTAGCGGGTTTGAGTTTTATCACATTGCCATGGAAATGCTGAAGGGTGATAAACAGTCAGCAGGAAGGGAGAAAAGAAAGACATTCGAGGAAGAGTTCGTGAAGGAAGACCCCACAGCAGAACCATCCCTAAACACTGAGAATGTAGCACCACACAGGAGTGTAGCATCAGTAACCTTTCCCCCGCCGCCTCCCTTTTCCTCAGCAGTCCGCTGGAAACAGATCTATACTTGAAAGGATGGGGGCAGGCCAGGGTAGGACCACCCCACAGATCTGTTAATTAAAGGAACTGGAACTGGAACTGGATTTACCCAGTGGCTTTCTACCATTAAATTGAATTCTTTAAAATTGTGGCATGAAGTGCAGTTAATGATGGGAATGCAGTGATTGGACTGTAACGATCTCTCTGTCCTTACACCACACACACACACACACACACACACACACACACACACACACACACACACACAAGTGTGGACGAGGCTTTGGGCTATCAGAGAATCCTATACCTGCAGCAAAATGCCACGGGCGCTTAGATCGGCACAGTGCCTTGGGGATAATGGCAAGAAGGGGTGCTAGAAAGTACGGGTGTGTTCTGGGAAAGAGAGCTGCTGCTGTCAGTACAGAGAACGGAGGCGCTGAAAACTCAGGTGCAGCAGCCACGCCTGAGACTTGACACAGGTTGGCCTTGTCCTATGTACAGCCACTGATTCCCTTGGGTGGAACGAACACATGCCAGGGTAAAACTGAATCCCTGGGAGGCACAAAAAGCGGGAAGTAAACGTCAAAAGTAAAACTAGAATTTTGAACCCAAAGCAGATCACTAAGCAGAGCTTGCCTAAACTTCTCTTAAAACACTACCCAGCCTTCCCAAGTACATTCCAGTGTTCTGTTCTGGGTGGGGCTGTCTAGATTCTGGTCCTTTTGGAATACTTCTTCCTAAGTGATAAGATGCAACCATTTTCGAAAAGCTTTGTTTTTATGGCTTTTTAAGCATCATTTTGCATTCAGAGCATGAGAGATGTTTAATTATTGTCCCGCGAGTCATTTCAAAATTCTATGTGACTCAGAAAAACGCGATGTTATTTTTATCTCCAGCATCAAGTTTTATGCTGTGTCTTTGATAATGTGGTTCTTTTTGGTGTGTAAAATAATAGTCATTTATGTAATCCCGGGGTCTATATGACTTTCATATTTCTTTCCTTCTCTTATTCTTACTTGACTTTGGGTTTTCTTTCTTGGCTATGACAGTGACCTTTCTACCCAACTTTAAGAATGTGCTTTTCAAAGTCAGAATTGGACAGTTTATTATCTGTGTCCTTTAAAGATAAAGCAAACCAAGTAGTACAACCACATGGGTTTATCTTTTAATTAAAACACAATTTCCTATATGTTTTAGGCTGAAAACATTATTTCCTATATATTTTAACAAGACAAACTCAGATTTGACTGTGTACGGTTTCATCTCTATCGATTAACAGAACCAGTTATTGTGATATCTGGCATACAATACTTACACCATACATAGTACAGCCCGGATAATTCTGATTTTATTTTAATAAGGTCAGTGATAATCAGGGGAGTAGAACAAGTAGAAAATTGTTCCCAAGGGGATATTAAAAGTGGAGATAATCTAATCCTCCAAGGTACGATGTGTTGACCTGGTAATTTCAGATATGATTTTATCACTCCGAGTCGGGTGCCTCCTGAGACTCGCTTCAGAACAACCCAAGATGATTTTCACTGTCAGCCAGGAACACTAATAAAATTGTTTTTCCTGCAGGCTAGTGTGTTAGGAAATTAAATTTATCTAATTATACAAATTGCACTGTCGCTTTTCACGTTGTAATTAAAATACGTCTTGTCAGGTCTTGCCTCTTTCCAGAAACCATTGGTTGACTATCTCTGTGTTATGTCTTCTCAG
Seq C2 exon
AGAACGGTGCAGAAAAACGCAAAATATGTTTGCTTGGCAAATAAAAACTGCCCGGTAGACAAGAGACGTCGAAATCGATGTCAGTACTGCAGGTTTCAGAAGTGTCTCAGTGTCGGGATGGTGAAGGAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000005964:ENSRNOT00000008302:3
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.555 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0253517=Zip=WD(100=34.8),PF0010513=zf-C4=PU(38.6=8.5)
A:
NA
C2:
PF0010513=zf-C4=PD(58.6=93.2)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
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]