RnoEX6034153 @ rn6
Exon Skipping
Gene
ENSRNOG00000007607 | Nr4a1
Description
nuclear receptor subfamily 4, group A, member 1 [Source:RGD Symbol;Acc:620029]
Coordinates
chr7:142905758-142917294:+
Coord C1 exon
chr7:142905758-142905933
Coord A exon
chr7:142915498-142916372
Coord C2 exon
chr7:142917165-142917294
Length
875 bp
Sequences
Splice sites
3' ss Seq
TGGGTCTCCTCCCTCTCCAGAGA
3' ss Score
9.19
5' ss Seq
AAGGTATTT
5' ss Score
7.64
Exon sequences
Seq C1 exon
GGAGACAGTTCCCATCCAGAGTCTGCTCAGCCAGTGCATGGCCTCAGCTGGGAAGGACAGGCTGGCCAGCTGTCACAGCTCCCCACTGGGTTCCTTGAGGCTGTGGAAAAGACCCCTCCCCCCCAACTAACCCTGGATTCTTCTTTTGCCCCCTGGGTCTGTGAAGATACACACTG
Seq A exon
AGATGCCCTGTATCCAAGCTCAATATGGAACACCAGCAACCAGCCCAGGACCGCGTGACCACCTGACAGGTGACCCCCTGGCCCTTGAGTTCAGCAAGCCCACCATGGACCTGGCCAGCCCCGAGACGGCGCCCACCGCACCTGCCACCCTGCCCAGTTTCAGCACCTTCATGGACGGCGGATACACCGGAGAGTTTGACACCTTCCTATACCAGCTGCCGGGGACAGCCCAGCCGTGCTCCTCGGCCTCCTCCACATCTTCTTCCTCGTCCTCGGCCACCTCTCCCGCGTCGGCTTCCTTTAAGTTTGAGGACTTTCAGGTGTATGGCTGCTACCCTGGCACCCTGAGCGGCCCATTAGACGAGACCCTGTCCTCCAGTGGCTCTGATTACTATGGAAGCCCCTGCTCAGCCCCGTCACCACCTACACCCAACTTCCAGCCATCCCAGCTCTCCCCTTGGGATGGTTCATTTGGCCACTTCTCCCCCAGCCAGACTTATGAAGGCCTTCGGGTATGGACTGAGCAGTTGCCCAAGGCTTCCGGGCCTCCGCCACCTCCAACCTTCTTCTCCTTCAGTCCTCCCACCGGTCCCAGCCCCAGCCTGGCCCAGAGTTCCCTGAAGTTGTTCCCAGCACCAGCCACCCACCAGCTAGGGGAGGGGGAGAGCTATTCCGTGCCAGCCGCTTTCCCGGGCTTGGCACCCACCTCTCCGAACTGTGACACTTCCGGCATTCTGGACGCACCCGTAACCTCCACCAAGGCCCGCAGTGGGTCTTCAGGGGGCAGTGAGGGCCGCTGTGCTGTCTGTGGAGACAACGCTTCGTGCCAGCATTATGGGGTCCGCACCTGTGAGGGCTGCAAAGGCTTCTTCAAG
Seq C2 exon
CGCACAGTACAGAAAAGTGCCAAGTACATCTGCCTGGCAAACAAGGACTGCCCTGTGGACAAGAGGCGGCGGAACCGCTGCCAGTTCTGTCGCTTCCAGAAGTGCCTGGCTGTGGGCATGGTGAAGGAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000007607-'1-4,'1-3,11-4=AN
Average complexity
A_C2
Mappability confidence:
100%=100=100%
Protein Impact
ORF disruption upon sequence exclusion (Ref, Alt. ATG (<=10 exons))
No structure available
Features
Disorder rate (Iupred):
C1=NA A=0.460 C2=0.000
Domain overlap (PFAM):
C1:
NA
A:
PF0010513=zf-C4=PU(38.6=9.3)
C2:
PF0010513=zf-C4=PD(58.6=93.2)
Main Skipping Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GGAGACAGTTCCCATCCAGAGT
R:
CTTCCTTCACCATGCCCACAG
Band lengths:
306-1181
Functional annotations
There are 3 annotated functions for this event
PMID: 22002310
Encodes an experimentally validated Eukaryotic Linear Motif (ELM). Method: alanine scanning. ELM ID: ELMI002018; ELM sequence: SATSPA; Overlap: FULL
PMID: 22002310
Encodes an experimentally validated Eukaryotic Linear Motif (ELM). Method: alanine scanning. ELM ID: ELMI002019; ELM sequence: SAPSPS; Overlap: FULL
PMID: 22002310
Encodes an experimentally validated Eukaryotic Linear Motif (ELM). Method: alanine scanning. ELM ID: ELMI002306; ELM sequence: SPSTPS; Overlap: FULL
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]