RnoINT0102986 @ rn6
Intron Retention
Gene
ENSRNOG00000007607 | Nr4a1
Description
nuclear receptor subfamily 4, group A, member 1 [Source:RGD Symbol;Acc:620029]
Coordinates
chr7:142915498-142917294:+
Coord C1 exon
chr7:142915498-142916372
Coord A exon
chr7:142916373-142917164
Coord C2 exon
chr7:142917165-142917294
Length
792 bp
Sequences
Splice sites
5' ss Seq
AAGGTATTT
5' ss Score
7.64
3' ss Seq
CCCCCCCCCCCCCCCTCCAGCGC
3' ss Score
11.23
Exon sequences
Seq C1 exon
AGATGCCCTGTATCCAAGCTCAATATGGAACACCAGCAACCAGCCCAGGACCGCGTGACCACCTGACAGGTGACCCCCTGGCCCTTGAGTTCAGCAAGCCCACCATGGACCTGGCCAGCCCCGAGACGGCGCCCACCGCACCTGCCACCCTGCCCAGTTTCAGCACCTTCATGGACGGCGGATACACCGGAGAGTTTGACACCTTCCTATACCAGCTGCCGGGGACAGCCCAGCCGTGCTCCTCGGCCTCCTCCACATCTTCTTCCTCGTCCTCGGCCACCTCTCCCGCGTCGGCTTCCTTTAAGTTTGAGGACTTTCAGGTGTATGGCTGCTACCCTGGCACCCTGAGCGGCCCATTAGACGAGACCCTGTCCTCCAGTGGCTCTGATTACTATGGAAGCCCCTGCTCAGCCCCGTCACCACCTACACCCAACTTCCAGCCATCCCAGCTCTCCCCTTGGGATGGTTCATTTGGCCACTTCTCCCCCAGCCAGACTTATGAAGGCCTTCGGGTATGGACTGAGCAGTTGCCCAAGGCTTCCGGGCCTCCGCCACCTCCAACCTTCTTCTCCTTCAGTCCTCCCACCGGTCCCAGCCCCAGCCTGGCCCAGAGTTCCCTGAAGTTGTTCCCAGCACCAGCCACCCACCAGCTAGGGGAGGGGGAGAGCTATTCCGTGCCAGCCGCTTTCCCGGGCTTGGCACCCACCTCTCCGAACTGTGACACTTCCGGCATTCTGGACGCACCCGTAACCTCCACCAAGGCCCGCAGTGGGTCTTCAGGGGGCAGTGAGGGCCGCTGTGCTGTCTGTGGAGACAACGCTTCGTGCCAGCATTATGGGGTCCGCACCTGTGAGGGCTGCAAAGGCTTCTTCAAG
Seq A exon
GTATTTTGTTGTTCCGAGCGACTACATCCTGTTGGAGGTGGGGATGGAGTGGATCATCTGTTGGGATCTGTAGTGACCTCCCTTGAGGTTCCTTCCCAGATGGTTCTGTCCTGCAGGAAGGGGACAGGTGTACTATCTTAGGGACTGGGACTTTCTAATTCAGCAGGGCACACAGCTCTCTAGGGCTGCAGAAAGCTGGGGAAGGGGGCAGAAGGTGTGTGTGTGGCCTGCAGTGGTGCTCGGGAACAGAAAATCTAGTGGGCAGCCTCTGGCTCTCCCCCGCCCCCATCCTGGGGGGCGAGGGGGCCACAGGCACTTGTGTTCCTGGCACTGGATGAAAGGACACAGGCAGAGGGTTCGGTTCTTGCTGGGGGTGGACTTAGGAACAGGCTGTGTGTTTGTCCCAGTGCTGGGTGCCTGCTTGACTTCCCCTCCCACCTCCACCCTCTTAGCTCTCTCCTCTGTGCTCCAGGAAAGGACAGGTGGACACTCGCAGACAACCTGTTAGAAAAGGTGTCTGGATGGCCTTGGGAGTCCCTAGTCTTTGGTCTTGGGGTCTGGGATCTTCCATTTGAGGTAGAAACCTCCTCCAGTATCTCCCAGACTCCTCTCCCTGCTCTGGCCCTCCATTCTCCCTCCCCTGCACCCAAATGTTAGGAAAATAGCTATGAACAGAGAGTGCTTTTGTCTGCATTGGCCACAGGATCTGGACGGTCCCCTCCCCTGGGCTCCCCCACCCCAGCCTCATGCTCTGACAGCCTGTTCCGTGTCCCCCCCCCCCCCCCCCTCCAG
Seq C2 exon
CGCACAGTACAGAAAAGTGCCAAGTACATCTGCCTGGCAAACAAGGACTGCCCTGTGGACAAGAGGCGGCGGAACCGCTGCCAGTTCTGTCGCTTCCAGAAGTGCCTGGCTGTGGGCATGGTGAAGGAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000007607:ENSRNOT00000010171:2
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.460 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0010513=zf-C4=PU(38.6=9.3)
A:
NA
C2:
PF0010513=zf-C4=PD(58.6=93.2)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Mouse
(mm9)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TAGGGGAGGGGGAGAGCTATT
R:
CTTCCTTCACCATGCCCACAG
Band lengths:
354-1146
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]