BtaEX6020589 @ bosTau6
Exon Skipping
Gene
ENSBTAG00000000507 | NR4A1
Description
Bos taurus nuclear receptor subfamily 4, group A, member 1 (NR4A1), mRNA. [Source:RefSeq mRNA;Acc:NM_001075911]
Coordinates
chr5:27980981-27985786:-
Coord C1 exon
chr5:27985530-27985786
Coord A exon
chr5:27981924-27982801
Coord C2 exon
chr5:27980981-27981110
Length
878 bp
Sequences
Splice sites
3' ss Seq
TTGGTCTCTTCCCTCTCCAGAGA
3' ss Score
10.14
5' ss Seq
AAGGTACTG
5' ss Score
8.56
Exon sequences
Seq C1 exon
CTGGCCGCCTCCCGCCGGAACCGCGCCGCCCCCCGCGCCCTTGTATGGCCAAAGCTCGCCGGGCCGCGTGCGTCAGTGGCGCCTCCGCCCCTCCCCGTGCGTCACGGAGCGCTTAAGAGCAGGGTCCGGCGCGGCCGGGAGTCCCAGTGGTGGAGGCTGCGAAAGTTGGGGGAGTGTGCAAGACAGCGGGAGCGTACGCGGGACCAGGCTGCGACTTGGGGCGCCGGTCCCGGGCAGGGGGAGCAGAAGCCAGCCGG
Seq A exon
AGATGCCCTGTATCCAAGCCCAGTATGGGACACCAGCACCAAGCCCAGGACCCCGTGACCACCTGGCAGGCGACCTCCTGACCCCTGAGCTCAGCAAGCCCACCATGGACCTGGCCAGCCCCGAGGCAGCCCCCGCTGTCCCTACCGCCTTGCCCAGCTTCAGCACCTTCATGGACGGCTACACAGGGGAGTTTGACACCTTCCTCTACCAACTGTCAGGCACAGCCCAGCCGTGCTCCTCTGCCTCCTCCTCGGCCTCCTCCACGTCCTCATCGTCAGCCACCTCCCCAGCCTCTGCTTCCTTCAAGTTCGAGGACTTCCAGGTGTACGGCTGCTACCCTGGCACGCTGAGTGGCCCTCTGGACGAGACCCTGTCCTCCAGCGGCTCTGACTACTATGGCAGTCCCTGCTCTGCACCGTCACCATCCACGCCCAGCTTCCAGCCTCCTCAGCTCTCTCCCTGGGATGGCTCCTTTGGCCCCTTCTCGCCCAGCCAGACTTACGAAGGCCTGCGGGCATGGACAGAGCAGCTGCCCAAGGCTTCTGGGCCCCCCCAGCCGCCGGCCTTCTTTTCCTTCAGCCCTCCCCCCGGCCCCAGTCCCAGCCTGGCCCCAAGCCCCCTGAAGCTGTTCCCCTCGCAGGCCGCCCACCAGCTGGGGGAGGGAGAGAGCTATTCCATGCAAACAGCGTTCCCAGGCCTGGTGCCCACTTCTCCCCACCTTGATGGCTCAGGGAGGCTGGACGCGCCTGTGACCTCTGCCAAGGCCCGGAGTGGGGCTCCGGGTGGAAGCGAGGGCCGCTGTGCTGTGTGTGGGGACAATGCTTCCTGCCAGCATTATGGGGTCCGCACCTGTGAGGGCTGCAAAGGCTTCTTCAAG
Seq C2 exon
CGCACAGTGCAGAAAAATGCCAAGTACATCTGCCTGGCTAACAAGGACTGCCCTGTGGACAAGAGGCGGCGAAACCGCTGCCAGTTCTGCCGCTTCCAGAAGTGCCTGGCCGTGGGCATGGTGAAGGAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000000507-'15-8,'15-7,23-8=AN
Average complexity
A_S
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=0.572 C2=0.000
Domain overlap (PFAM):
C1:
NA
A:
PF0010513=zf-C4=PU(38.6=9.2)
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:
CCCTTGTATGGCCAAAGCTCG
R:
CTTCCTTCACCATGCCCACG
Band lengths:
350-1228
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]