DreINT0106143 @ danRer10
Intron Retention
Gene
ENSDARG00000000796 | nr4a1
Description
nuclear receptor subfamily 4, group A, member 1 [Source:ZFIN;Acc:ZDB-GENE-040704-11]
Coordinates
chr23:32228697-32229709:-
Coord C1 exon
chr23:32228916-32229709
Coord A exon
chr23:32228827-32228915
Coord C2 exon
chr23:32228697-32228826
Length
89 bp
Sequences
Splice sites
5' ss Seq
AAGGTAAGA
5' ss Score
10.57
3' ss Seq
TTTCCTCAATAATTCTGTAGCGC
3' ss Score
6.56
Exon sequences
Seq C1 exon
AAATGACCTGTGTTCAAAGTCAACATGGAGTCCAGTCCTACGAGAGCTCCCTCTTCAGCTCAGAGTTTCTGAATCCTGACTTCACCTCCAGGTTGGCCATGGATGTGACCGAGCAGCGGGAACAGCTCTCTGCGCCCTCCCTACCCAGCATCACTTCTCTGGTTGGGGGATACGTTGGCGAGTTTGACACCTACTCATGCCAGATCGCCACAGGAGCTGCTTCTACCTGTGTGGGCAGCACCTCCGGGCAGCTGGACTCCTTCAAGCTGGATGACCTCCAGGTGTATGGCTGCTACCCGGGCACGTTTGCTTTGAGCTACCTGGACGAGACGCTGTCCTCTTCGGGTGGGTCAAACTGCTTTGGAAGTCCGGCATCTGCACCGTCTCCCTCCACCCCGGGATACCAGCACATGTCTGCATGGGACAGCACCTTTGGTCCCTGCTCTCCTGACGAGGGTTGCTGGGGTTCTGAGAAGCCTCTGAACCAGGCAGCATCTTTCTTCACATTTGGGCACGTCACGGCTGATGAGCTTTCCCCACTGGGACAGATGCAGTCACAGATCCCAGATCAGGATCCCTTTTCTCATACTCCGCAACATGGTTCTCCACTTCCCTTCAGTCCACTCAGCTTAGAGCAGGGCAGCCGGGATGGATCGGGACTGATGGACGGACACTTGTCTCCTAAAGTGAGGAGCCCCACAGGAAATGAGGGACGCTGCGCCGTGTGCGGAGACAATGCTTCTTGTCAGCATTACGGGGTGCGCACTTGTGAAGGATGCAAAGGCTTTTTCAAG
Seq A exon
GTAAGAAAGAGAAATGCTGTGATCATGCTGTTGGTTTTGGCCATTAGGCTTGATTTATAACATTCAATGTTTCCTCAATAATTCTGTAG
Seq C2 exon
CGCACAGTACAGAAGAACGCCAAATATGTTTGTCTCGCCAACAAAGACTGTCCAGTGGATAAAAGGCGGAGAAACAGATGCCAGTTCTGCCGCTTCCAAAAGTGCCTAGCTGTGGGGATGGTGAAGGAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000000796:ENSDART00000000876:2
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.282 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0010513=zf-C4=PU(38.6=10.2)
A:
NA
C2:
PF0010513=zf-C4=PD(58.6=93.2)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GGATGGATCGGGACTGATGGA
R:
TGGCGTTCTTCTGTACTGTGC
Band lengths:
170-259
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]