DreINT0106194 @ danRer10
Intron Retention
Gene
ENSDARG00000014480 | nr6a1b
Description
nuclear receptor subfamily 6, group A, member 1b [Source:ZFIN;Acc:ZDB-GENE-040724-202]
Coordinates
chr21:8162658-8163012:+
Coord C1 exon
chr21:8162658-8162779
Coord A exon
chr21:8162780-8162859
Coord C2 exon
chr21:8162860-8163012
Length
80 bp
Sequences
Splice sites
5' ss Seq
AAGGTAATA
5' ss Score
8.49
3' ss Seq
TTTGAGTTTGTGTTTTGCAGAGA
3' ss Score
7.32
Exon sequences
Seq C1 exon
GTTTGGTGAGGATGCTATGGAGGTCATGGAAAGCTTAAATTTTCTCTTCCGTAAGTTTCATCAACTAAACATCAGCAATGAGGAGTACAGCTGCTTAAAGACCATCACGCTGCTTAATCAAG
Seq A exon
GTAATAACACACACACACACTAACCCTGATCCTTTTGTTTTTGACAACAGGTGTGTGTAATTTGAGTTTGTGTTTTGCAG
Seq C2 exon
AGACGACAGGTTTGTGCAACACGTCAATGCTGAAACAATTAAGTGAACGTTACTGGACGCTGTGTCGTGAGCTGACAGAACGACTTCATCCACAGCGACCCAAACGCTTCTCTGACATCATCACCTGCCTTACTGAGATACGCCACACGTCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000014480:ENSDART00000122773:6
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=0.000
Domain overlap (PFAM):
C1:
PF0010425=Hormone_recep=FE(21.0=100),PF113923=DUF2877=PU(40.0=90.5)
A:
NA
C2:
PF0010425=Hormone_recep=FE(26.2=100),PF113923=DUF2877=FE(53.7=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:
TGGTGAGGATGCTATGGAGGT
R:
ACAGCGTCCAGTAACGTTCAC
Band lengths:
182-262
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]