RnoINT0103025 @ rn6
Intron Retention
Gene
ENSRNOG00000013232 | Nr6a1
Description
nuclear receptor subfamily 6, group A, member 1 [Source:MGI Symbol;Acc:MGI:1352459]
Coordinates
chr3:23035558-23037291:-
Coord C1 exon
chr3:23037170-23037291
Coord A exon
chr3:23035711-23037169
Coord C2 exon
chr3:23035558-23035710
Length
1459 bp
Sequences
Splice sites
5' ss Seq
AAGGTGAGT
5' ss Score
10.47
3' ss Seq
TTTGTTTTTATTTTTTTCAGATA
3' ss Score
10.77
Exon sequences
Seq C1 exon
ATTTAGTGATGAAGGGATGGAGGTGATTGAACGACTCATCTACCTGTATCACAAGTTCCATCAGCTAAAGGTCAGCAATGAGGAGTATGCATGCATGAAAGCAATTAACTTCCTGAATCAAG
Seq A exon
GTGAGTCGGTGGGAGGGCAAGAGCAGTGGTTTGTATTATGTATTTATTTTTGCCAGTAAGCTTTGCCCTTCTGTATCACATACACAACTCCCAATCCCCCCACCCCCACTTCCCACCCCTAGGACTGTCACAGAATCTGTCACACCATGTGACCATCAGTCTTGGAAGGCCTACATTTCCCCTAGTCATGGCCCTGCTACTCTACAGTGCAAGGCATTCTTAGTTTTGGTTTTGTGTGTGTGTGTGTGGTTTTTTTTTTTTTAAATCTAAATGCCACAATCTCTATAACTCACAGAGGAAGGAAGAGGATTCACTTTGTTTAGTCAGTTTTAATGCATTTAAACACAGACACCAAGGACAGAACATGCGTCATTTAAAATATGTACAAGTTTACTAGCAACTGAAGAGCAGGGTGACTGATGAGGCTGCTGGAGATAAGGCTGGTTGACAGGCTGACCATGGCTCTCATGTCGCAGGGAAGAGTGGTGGCACACAGACCTCCGTGTGCACATGAAGCCCGCTCTTCCATCAGAGGAGTCCAATGATTTATAGGCATATTGCCAACAAGTGGCATGTGACAGTTACTGGTAACTGGCTTGTGAGAGAAAATTGGTGTTCTTTTATAAAAAGTAGCATACAAATGCCCCACTCCCAGAGTGGACCTGAGAGATTTTGTTCCTGTAGCTTTAAAAGTGCTCTGTTTTCCAATCTGGGGACTTTTCATCGGTCCTTCCTTTCTACCACTATTCCCCACTCAACCTTGCAGTGCTGTATAAACCTACTGCTCCTGTCTGTATTCCATCAAGCATTTATCAGGCAACCTACATGCCTTCTCCAGCCAAGCCCTATACCATGTGGTAAGGATATTGCAGAGGTTGGGGGAAGGAGAAAGATAAAACCCAGGCCAACCCTCAGGTCCCTGAAAAATCCACATCCCAGTAACACTCAACACATTAATTGTACTATAAATGGGATAAGATTGGTAGAACTTCTTAGAGGAGGAAAAATGTTTGTAGACCCCAAAGATTTGGTATACTTTACATGCAGAATGCTTTATTCATTTCCTGTACTTTAGACGTGTGTGTGTACATCAAGACAGAATAGTAAGAACACAGGGGCATTGGAGATGATACGTGTCAGGCTCCAGACAACCTCTGCTTCAAAGATGCTCAGAAGGGTTATGGGTAAGGAGGTAGTCACTTGTTCACACTTGCTGGTGCCTGTCTTGTGCCACCATACCCTTTATTAAGATCTTAGCACTCTAGGGTACTGGCAAAGGGCTGTCTTTTACATATTTTTCCTTTTCTATCTTTATTTTCCCTTATCTGGATCTTAGTTTCTCCACATTAGAAAAAGAAAAATCTTTGTTATGACCGTATTTAACAATGTCTAATTTTTTACAAATCTGATTTCCACCCCCTCATTCCTTAGCTGATTTTTTTGTTTTTATTTTTTTCAG
Seq C2 exon
ATATCAGGGGTCTGAGCAGTGCCTCACAGCTGGAACAACTGAACAAGCGGTATTGGTACATTTGTCAGGATTTCACTGAATATAAATATACACATCAGCCAAACCGCTTTCCTGATCTGATGATGTGCTTGCCAGAGATCCGATACATCGCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000013232:ENSRNOT00000018751:7
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=FE(21.2=100)
A:
NA
C2:
PF0010425=Hormone_recep=FE(26.4=100)
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:
TTAGTGATGAAGGGATGGAGGTGA
R:
CGATGTATCGGATCTCTGGCA
Band lengths:
270-1729
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]