RnoINT0103007 @ rn6
Intron Retention
Gene
ENSRNOG00000012682 | Nr5a1
Description
nuclear receptor subfamily 5, group A, member 1 [Source:RGD Symbol;Acc:68350]
Coordinates
chr3:23013937-23016566:-
Coord C1 exon
chr3:23016425-23016566
Coord A exon
chr3:23014566-23016424
Coord C2 exon
chr3:23013937-23014565
Length
1859 bp
Sequences
Splice sites
5' ss Seq
AAGGTGCGC
5' ss Score
9.05
3' ss Seq
CAGACTGCTCCTGCCCACAGCTG
3' ss Score
8.43
Exon sequences
Seq C1 exon
GGCTTCTTCAAGCGCACAGTCCAGAACAACAAGCATTACACGTGCACCGAGAGTCAGAGCTGCAAAATCGACAAGACGCAGCGTAAGCGCTGTCCCTTCTGCCGCTTCCAGAAGTGCCTGACGGTGGGCATGCGCCTGGAAG
Seq A exon
GTGCGCGTCCTGCACGCCCGGGACCCCTGACTGCTGGCCGCCCCCAGGGAGCCGCGGGCGGGCCTGGGAGAGGGGCTGAGGGGAAAGCCGAGCAGTTTCTGGATCCAGGTGATTGGCCCCTCGGCGTGACGTTGGGGCCCCAGCTCTGCAGGGAACAGAGGCAACTAAGGGAGTCTAGCGCCAGAAGAGTCCGTGCGTGTAGGGCCTGCCTGGGCTCAGTCCCAAAATATCAAAAGTAAGACTTCCGGCATGGTGGTCCATCCCTGCAATCCCAGGACTCGGGAGACTAAGACAAGGCCAGTCATGAGTTGCGTATTGAGATCCAGTATCCCGTCCCTCGAGGGGGTTAAGTCTTTCTCCAGGACAGAGCTGACCCCCAATGACTCACTGTGTGAGAAGCTCCCAGACACCCCCATAGATTCCCCACACCAGCCAAAGCCTCAGCTCTCAATAACTTGACCATGTTCAAATTCCAGCTGTATCACTTGTAGGCTAGGGACTTCGCTGAGCTGCAGATGCCCCCATTTGAATAACGAAGTAAAAAAGTAATGCTTGTCTTGTGTTAGTGGGAGGCCTGGGGGTGGGGTGGGGGCGGCAAGCAAAAGCGGGAGTTGCCTGCTGTGAGGGGAAAGACTCAGTAGAATAGCTGGAACTGTCATTATTATCACCCTTTCTGCTGCTGTTTGTCCATCGCTGTTCAGACTGTGCATCTATCTGTCTGTCCAGGCATCTAAGTTTCACAGGAATTGAGGTTCCTTCCCATGCATTCTGAGTCCAGCCCTGACTCAGGGTTGGGGTGAAGGGAACAATGGCCTATGGCTACCTCTCCCCTCCTGTTCTGGTCCAGAGAAGACAGCAACAGTCCATTAGGTCCAGACTCAGAAAGTGGACAGTCATAGCTTCTACCCTCCTGGCCTCAGTCGGGCTGAGCGCCCAGCCGGCAGCTGTTGGCTAAAGTTTTTGCAGAGAAGGTCCCAGAGGCTGGGGAAAGCTGTGGCCATAGCCTGCTACCTAGAGAGGGACTCGGATTGAAGGAGGTACCCTGTCCTGTGTGGGGAGCCCCCCTAGGTCCAGGTCCTGAGCAGGCGGAGAGCTGGCTATTGTGGGTGGCAGCAGCCTGTGCCGGCAGCCTGAGGGAGCGCAGAATGCTGTTCACCTCCAGGCAAGAAGATCTATGTCGGGCAGGCTCCCAAGTTCTGTGGAACACCACCCCTCTCTCCCTTTTCTTCGAGCTTGGGTGGGGTCCTGTCTGAGCAAGGGCTGGAACCACACTGGAGCTGCAGAAATGCACCTGTTGAGTCTGGCGGGTGACACATTCTTGGCCAGGAGAAAAACATCTGGTCAGCAGAATAAATCCCCTCCTCCAGCACAAATCCAGGCTCACAGCAGAGGGCAGTTGGGGAAGCTTTGTAGAGTCGAGAAGGCACCCCACTGTGAGCAAAGCAGGGCTCCTTTGCTTTCACCATCTCCCTGTCAGACCAAGGTCCAGGCACCCAGGAGCTCTCAGCCTGAGGTATTCATATGGGGTAGGACAGGAAATTCTGCCTGGGGGAATCCGGAGACTTCCTGGAGGTGGCAACGTTGGACTGGGTGTTAAGAAATTGCAAGGGAAAGAAAGGGGTTTCAGGCAGAGGGGAGGGTAGGTGAGTGGGCAGAGGGGAAGTAGATCCGCTCATGAGAATGTGGAGGAAGGCCTGGGATGCCAAGCCAAGGCTGTTGCTCTCACCTGTGGGCAGAGAAGGCCACTGAATACGGCTGGGGGGGGGTGTTATATGCGTGTGTGAGACATACCTTTTTGGGAAGGATCTGTGGCAGACAGTTGGGGAAGGTGAAACCTGACAGACTGCTCCTGCCCACAG
Seq C2 exon
CTGTGCGTGCTGATCGAATGCGGGGCGGCCGGAACAAGTTTGGGCCCATGTACAAGAGAGACCGGGCCTTGAAGCAGCAGAAGAAAGCACAGATTCGGGCCAATGGCTTCAAACTGGAGACCGGACCACCGATGGGGGTTCCCCCGCCACCCCCTCCCCCACCGGACTACATGTTACCCCCTAGCCTGCATGCACCGGAGCCCAAGGCCCTGGTCTCTGGCCCACCCAGTGGGCCGCTGGGTGACTTTGGAGCCCCATCTCTGCCCATGGCCGTGCCTGGTCCCCACGGGCCTCTGGCTGGCTACCTCTATCCTGCCTTCTCTAACCGCACCATCAAGTCTGAGTATCCAGAGCCCTACGCCAGCCCCCCTCAACAGCCAGGGCCACCCTACAGCTATCCGGAGCCCTTCTCAGGAGGGCCCAATGTACCAGAGCTCATATTGCAGCTGCTGCAACTAGAGCCAGAGGAGGACCAGGTGCGTGCTCGCATCGTGGGCTGCCTGCAGGAGCCAGCCAAAAGCCGCCCTGACCAGCCAGCGCCCTTCAGCCTCCTCTGCAGGATGGCGGACCAGACCTTTATCTCCATTGTCGACTGGGCACGAAGGTGCATGGTATTTAAGGAGCTGGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000012682:ENSRNOT00000017651:3
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=0.538
Domain overlap (PFAM):
C1:
PF0010513=zf-C4=PD(64.3=93.8)
A:
NA
C2:
PF0010425=Hormone_recep=PU(19.8=19.5)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Human
(hg19)
No conservation detected
Chicken
(galGal4)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GCTTCCAGAAGTGCCTGACG
R:
CAGGATAGAGGTAGCCAGCCA
Band lengths:
354-2213
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]