RnoINT0102990 @ rn6
Intron Retention
Gene
ENSRNOG00000007607 | Nr4a1
Description
nuclear receptor subfamily 4, group A, member 1 [Source:RGD Symbol;Acc:620029]
Coordinates
chr7:142918409-142920216:+
Coord C1 exon
chr7:142918409-142918587
Coord A exon
chr7:142918588-142919379
Coord C2 exon
chr7:142919380-142920216
Length
792 bp
Sequences
Splice sites
5' ss Seq
CTGGTGAGT
5' ss Score
10.1
3' ss Seq
CTCCACACTCCCTGCTGCAGATC
3' ss Score
7.18
Exon sequences
Seq C1 exon
ATCTAAGCCCGGTGAGGGGAAGCTCATCTTCTGCTCAGGCCTGGTGCTACACCGGCTGCAGTGTGCCCGCGGCTTTGGTGACTGGATAGACAACATTCTAGCCTTCTCACGGTCCCTGCACAGCTTGGGTGTTGATGTTCCTGCCTTTGCCTGCCTGTCTGCTCTGGTCCTCATCACTG
Seq A exon
GTGAGTGGCAGGTACCAGACTGGGCTCCCTAGAGTGCCTGCAACATTGGGATGTCAGGACCTGCATAGGGACTTAGCTCTACTCGCCCCAAAAGCTTAAATCAGCCTCTGAATGACCCCAGACTCCTCAGGATGTGACTGTAGGTGCTGGGCATCATCTAGTTTAGGGTTTGGGTTTGTTTTAAAACCTTCCTGTCCACCTCACAAGGCACAGAAGAGTGCACACATGAATGTTTCAGATTCTGCACTTGGATAGCCAGCGCCACAGTCCAGAAACAGGACTGGCATCGGCTCTCCGTTAGGCCCCCTCCTTATTGTCTCTGTAAGAGGCAGCCACTCTGCCAGACACAGTGGCGTTCCTGTTGTGGATTCTAGTGTGCGTATCACAGGGTATGGGCTCTAGTGTTCGGTGTAGACATGCCTGGGTCCCTTCTGCTCCTGCTCCCATTTCCACTTAGGCTTCTTAGGGGATAGAACAAGATCAGAAGAGCTGGGTGGAGCTTGAAGGGGTGGGTGGTAGCCCGAAGTCACTCCTGTGAGACTCTAGGATTTTAGAACAGCGTGGAACCTATACCCCAGAAAACCCAGGCTAGGGTTTTGTGTTGTTTGTCTGTACCTCAGCTAGCAATTCAAACTATCCGAGCCTGTCTCTCCCTTGCAACATTGTTAACACTCGTTTCAAATGTCGACTGGTCTGGAAAATGGGTTCCTTGTAGGATACGCTAGAGGGTCGGGGGAGCTTGAGAGGTGAGGGGGGTCAACCCGATAGCTAACTCCACACTCCCTGCTGCAG
Seq C2 exon
ATCGACATGGCCTCCAGGACCCTCGGCGGGTGGAGGAGCTGCAGAACCGCATTGCTAGCTGTCTGAAGGAACACATGGCCGCCGTGGCAGGAGACCCACAGCCGGCCAGCTGCCTGTCACGTCTGCTGGGCAAACTGCCTGAGCTCCGGACTCTGTGCACCCAAGGCCTACAGCGCATCTTTTGCCTCAAGCTGGAGGACTTGGTGCCCCCTCCACCTATCGTGGACAAGATCTTTATGGACACCTTGTCTTTCTGACCCTGCCCCGAACACGCGTGCACACTCACGTGCATGTTCTTCTTGTCACCCACGTGCCTTTAAGCCCATAGCCCACGGACCCCCAGACCACCCCACCCCCCAGCCTGTTTTTTGAGCTAAGACTGATGTATCTCCTCATTCCAGAAGATGGACAGAGAGAGAGAGAGAGCTCAAGACCTGGGGGGGAGGGTGTGTATTCACGGGGGTGACCCCACTATTTCTCTTATCCCTCCCAGCTCAGACCTGGCCTTCCGCGTGTTTTTGTAAGATAAACCATTTTTAACACATACCACTCTGCTGTATATAAGCTGACGCTGCTGTAAATACAGAAAGGAAGAGGTCGGGGTGGGGGTTTGAGAGGAAGGGTGGGCCCCCCAACCCCGCCAGCTGGGCAAGCCTCTCGAGCCTCCAACTTGAGATCTCTTCCGCTCTCCTTCCATGTGTACATAGCTGTCACTCAAGAAGGTGATTGACAGATTCTGATTTATATTTGTGTATTTTTTTCCTGGATTTATAGGATGTGACTTTTTCTGATTAATATATTTAATATATTAAATAAAAACTAGACATGTAGCTGAAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000007607:ENSRNOT00000010171:6
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0010425=Hormone_recep=FE(31.4=100)
A:
NA
C2:
PF0010425=Hormone_recep=PD(35.6=79.1)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Mouse
(mm9)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CCTGTCTGCTCTGGTCCTCAT
R:
GCTATGGGCTTAAAGGCACGT
Band lengths:
355-1147
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]