DreINT0106144 @ danRer10
Intron Retention
Gene
ENSDARG00000000796 | nr4a1
Description
nuclear receptor subfamily 4, group A, member 1 [Source:ZFIN;Acc:ZDB-GENE-040704-11]
Coordinates
chr23:32227844-32228826:-
Coord C1 exon
chr23:32228697-32228826
Coord A exon
chr23:32228008-32228696
Coord C2 exon
chr23:32227844-32228007
Length
689 bp
Sequences
Splice sites
5' ss Seq
AAGGTGAGG
5' ss Score
9.16
3' ss Seq
TATATTGTCCCTCTGTGTAGTTG
3' ss Score
7.18
Exon sequences
Seq C1 exon
CGCACAGTACAGAAGAACGCCAAATATGTTTGTCTCGCCAACAAAGACTGTCCAGTGGATAAAAGGCGGAGAAACAGATGCCAGTTCTGCCGCTTCCAAAAGTGCCTAGCTGTGGGGATGGTGAAGGAAG
Seq A exon
GTGAGGACAAAATTGTTTAAATCAACAAGTGGGAATACATGTGTGTTTTCAAGAGTTCACACTTAGCTGATGATTGATGATAAAGCTTGTTTGGCATGCTGTCCTGGGAGAAAGCCCTGAGTTTTTTTATGAGATCCTCAAGCTTTGGGCTCCCTCCCGTTAACAGGGAGTTTGAGCTCAGGTATATCTTGATGAACTCCCCCAACCTATTTCTAGCTAATGACAGATATAGGGATGGCTAAGGAGAGATATACGGCTTGCTAAGAGCTTGACTACGTTGTCAATTTGGTATGTTCAGTTTACTTAGGTTGCGTGTTTTTTGGACTGTCGGAGGAAGCCGGGGAAAACCCACGCAAGCACGGGGTGAATGAACAAACTCCGTACAGAAATGTCGACTGGTTTAGTAGAGACTTTAACCAGAGACATTCTTGCTGCAAGGCAACAGTGCTAATCACTGGGCCACCGTGTCGCCTCTCTAGAAAAGAAGGGGGAGTAGGTGTGGGTGGGGGGATTCTTTAAGAAAAAGATACTGAGATAAGAAACTCAATCAATCGTAAGCTAATGTGGGACCAGCTGTGATCAATCATGAGCATGTAATCCTTTTGAAATTAGTTTATAAATAAACTTCACTCATTGAATAACACACCTCAGACATTTTTAATAAGTGTGTATATTGTCCCTCTGTGTAG
Seq C2 exon
TTGTAAGAACAGACAGCCTGAAAGGAAGAAGGGGGCGTCTGCCATCCAAACCCAAAGCTGTTCAGGACTCAGTGTCTGTCTCTTCACCTGTGAACATCATCGCCTCTCTCGTTACTGCCCATATCGACTCAAACCCTGCCAGTGCAAATCTGGACTATTCAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000000796:ENSDART00000000876:3
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.200
Domain overlap (PFAM):
C1:
PF0010513=zf-C4=PD(58.6=93.2)
A:
NA
C2:
PF0010425=Hormone_recep=PU(0.5=1.8)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CGCACAGTACAGAAGAACGCC
R:
CTTTGAATAGTCCAGATTTGCACTG
Band lengths:
294-983
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]