DreINT0106145 @ danRer10
Intron Retention
Gene
ENSDARG00000000796 | nr4a1
Description
nuclear receptor subfamily 4, group A, member 1 [Source:ZFIN;Acc:ZDB-GENE-040704-11]
Coordinates
chr23:32227339-32228007:-
Coord C1 exon
chr23:32227844-32228007
Coord A exon
chr23:32227542-32227843
Coord C2 exon
chr23:32227339-32227541
Length
302 bp
Sequences
Splice sites
5' ss Seq
AAGGTAAGG
5' ss Score
10.51
3' ss Seq
TATTTTCGGTAATTGTCTAGTAT
3' ss Score
2.23
Exon sequences
Seq C1 exon
TTGTAAGAACAGACAGCCTGAAAGGAAGAAGGGGGCGTCTGCCATCCAAACCCAAAGCTGTTCAGGACTCAGTGTCTGTCTCTTCACCTGTGAACATCATCGCCTCTCTCGTTACTGCCCATATCGACTCAAACCCTGCCAGTGCAAATCTGGACTATTCAAAG
Seq A exon
GTAAGGAAAAAACACGCTTTACTACAACATAACAGAAAAATTAAGCTTGATTAGTGTTTTACCTTTAATAAATATATAGATTTCATTTTAATTACTTTAAATCAGGGGTATCCAGTACTGCTCCCGAAAGGCCACGTCCCTGCAGATTTAATAAACTAAACAATTAGTACATAACAGCCCAAGTCTTTTTTTTTCTGAGGAAACATCTGCAGAACAGTGGCCTTCCAAGAAACAGTTTGGACACCCCTGCCCTAAATATCAACATTGCTAATCAATGTACTTTATTTTCGGTAATTGTCTAG
Seq C2 exon
TATCAGGAATCAACATCTGGATTGCCTGAGAAGGAAGATGCCAACGACATACAGCAGTTTTATGACCTGCTAACAGGGTCAATGGATGTGATCAGGAAGTGGGCTGGAAGCATCCCTGGATTCAGTGCCTTTTGTAAGGAGGACCAAGAGCTTCTTCTGGAGTCAGCTTTTGTTGAGCTCTTCATACTTCGTCTAGCTTACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000000796:ENSDART00000000876:4
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.200 A=NA C2=0.015
Domain overlap (PFAM):
C1:
PF0010425=Hormone_recep=PU(0.5=1.8)
A:
NA
C2:
PF0010425=Hormone_recep=FE(33.8=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CAGCCTGAAAGGAAGAAGGGG
R:
ACGAAGTATGAAGAGCTCAACA
Band lengths:
343-645
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]