RnoINT0102993 @ rn6
Intron Retention
Gene
ENSRNOG00000005600 | Nr4a2
Description
nuclear receptor subfamily 4, group A, member 2 [Source:RGD Symbol;Acc:3202]
Coordinates
chr3:43115070-43116819:-
Coord C1 exon
chr3:43115954-43116819
Coord A exon
chr3:43115200-43115953
Coord C2 exon
chr3:43115070-43115199
Length
754 bp
Sequences
Splice sites
5' ss Seq
AAGGTGAGC
5' ss Score
9.6
3' ss Seq
TACATTCTCTCCCTCTACAGCGC
3' ss Score
11.08
Exon sequences
Seq C1 exon
CCATGCCTTGTGTTCAGGCGCAGTATGGGTCCTCGCCTCAAGGAGCCAGCCCCGCTTCTCAGAGCTACAGTTACCACTCTTCGGGAGAATACAGCTCCGATTTCTTAACTCCAGAGTTTGTCAAGTTTAGCATGGACCTCACCAACACTGAAATTACTGCCACCACTTCTCTCCCCAGCTTCAGTACCTTTATGGACAACTACAGCACAGGCTACGACGTCAAGCCACCTTGCTTGTACCAAATGCCCCTGTCCGGACAGCAGTCCTCCATTAAGGTAGAAGACATTCAGATGCACAACTACCAGCAACACAGCCACCTGCCCCCTCAGTCCGAGGAGATGATGCCACACAGCGGGTCGGTTTACTACAAGCCCTCTTCGCCCCCGACACCCAGCACCCCGGGCTTCCAGGTGCAGCATAGCCCGATGTGGGACGATCCGGGCTCCCTTCACAACTTCCACCAGAACTACGTGGCCACTACGCATATGATCGAGCAGAGGAAGACACCTGTCTCCCGCCTTTCACTCTTCTCCTTTAAGCAGTCGCCCCCGGGCACTCCTGTGTCTAGCTGCCAGATGCGCTTTGACGGGCCTCTGCACGTCCCCATGAACCCGGAGCCCGCGGGCAGCCACCACGTAGTGGATGGGCAGACCTTCGCCGTGCCCAATCCCATTCGCAAGCCGGCATCCATGGGCTTCCCGGGCCTGCAGATCGGCCACGCGTCGCAGTTGCTTGACACGCAGGTGCCCTCGCCGCCGTCCCGGGGCTCTCCCTCCAATGAGGGTCTGTGCGCTGTTTGCGGTGACAACGCGGCCTGTCAGCATTACGGTGTTCGCACTTGTGAGGGCTGCAAAGGTTTCTTTAAG
Seq A exon
GTGAGCAAGTCAGGGCGGCGGTGTCAGGTAGTGACCTTGTACCTGAGACCCAGCAGTTTGCCCTCACCTTCCGGTCAGCAGCCCAGCTCGAGTTCTGAAGCTACCCACGAGCTGTAGAAGAGGTTTCGGGGTGTCTAAGGAAAGAAATAAAGACTGGGAGAGTCAGGCTTTCACCTCCCCTCCCCCCCGCGCCCCACAGCAACCTGCGGGCCCCCGGCGGGCTCAAGCCCGAAATTGCTGAAGCCAGAGTTGGAAGAGGGCGATTTGCATGTGTTAGGCGCTGTCTTCCTTGTTCAGATTGAAATTGGTTAGGACAGAGAACCGTGTCTGAGCTAACCAAGTGGAACAGAATTCCCTATGGTCAAATTAAGTGATCTCTTTATTTCGCCATCCTGATTGAATAATCTTATCATTTTAAATAGAGAAGGTCTCCAAGGAATGTAAATAATATGAATGCCCACGGATTTGTATTTACCGAGCGTCTCCTGCTCCTTCTCCTGGCATATAAAACACAGCAAGGAGCGGCAAGGTTAGCTCAAATGTTAACGCTATCAATTTTCTTCTGGTAAATGCCCTGGGGAGGAAAAGGAAAGGAAATAGGAAGAAAAGAAAAAGGAAAAAAATTTAAGGAATAGTGTTTGTGTTTGTAGGGAAGGAATGCAGATCCAAGCCATTTTTTAAAAAATATGTCCAGTTTGCTGTAGTGTGAATTAAAATAATAATCATTTTGGGCCTACATTCTCTCCCTCTACAG
Seq C2 exon
CGCACGGTGCAAAAAAACGCGAAATATGTGTGTTTAGCAAATAAAAATTGCCCAGTGGATAAGCGCCGCCGAAATCGTTGTCAGTACTGTCGGTTTCAGAAGTGCCTGGCTGTTGGGATGGTTAAAGAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000005600:ENSRNOT00000041394:3
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.514 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0010513=zf-C4=PU(38.6=9.4)
A:
NA
C2:
PF0010513=zf-C4=PD(58.6=93.2)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TAGTGGATGGGCAGACCTTCG
R:
CAACAGCCAGGCACTTCTGAA
Band lengths:
345-1099
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]