DreINT0106146 @ danRer10
Intron Retention
Gene
ENSDARG00000000796 | nr4a1
Description
nuclear receptor subfamily 4, group A, member 1 [Source:ZFIN;Acc:ZDB-GENE-040704-11]
Coordinates
chr23:32227080-32227541:-
Coord C1 exon
chr23:32227339-32227541
Coord A exon
chr23:32227259-32227338
Coord C2 exon
chr23:32227080-32227258
Length
80 bp
Sequences
Splice sites
5' ss Seq
CAGGTGCGT
5' ss Score
9.73
3' ss Seq
AGATTTATTTATGCATTTAGGTC
3' ss Score
6.33
Exon sequences
Seq C1 exon
TATCAGGAATCAACATCTGGATTGCCTGAGAAGGAAGATGCCAACGACATACAGCAGTTTTATGACCTGCTAACAGGGTCAATGGATGTGATCAGGAAGTGGGCTGGAAGCATCCCTGGATTCAGTGCCTTTTGTAAGGAGGACCAAGAGCTTCTTCTGGAGTCAGCTTTTGTTGAGCTCTTCATACTTCGTCTAGCTTACAG
Seq A exon
GTGCGTCAGTTCAGATGATGTTCAGTTAAGCCTTATAATGGTATTTTATGAGATGACTAAAGATTTATTTATGCATTTAG
Seq C2 exon
GTCAAACCCTGAGACAGACAAACTTATTTTCTGCAATGGTGTGGTTTTGCACCGGACGCAGTGCGTACGAAGCTTTGGTGATTGGATTGACTCAATTATGGAGTTCTCTCAGAGTTTACATCGCTTGAATTTGGACATATCTGCTTTTTCCTGTCTTGCCACACTGGTCATAATCACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000000796:ENSDART00000000876:5
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.015 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0010425=Hormone_recep=FE(33.8=100)
A:
NA
C2:
PF0010425=Hormone_recep=FE(30.3=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GCTGGAAGCATCCCTGGATTC
R:
ATCACCAAAGCTTCGTACGCA
Band lengths:
183-263
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]