DreINT0106153 @ danRer10
Intron Retention
Gene
ENSDARG00000044532 | nr4a2b
Description
nuclear receptor subfamily 4, group A, member 2b [Source:ZFIN;Acc:ZDB-GENE-040718-103]
Coordinates
chr6:12229738-12230242:+
Coord C1 exon
chr6:12229738-12229901
Coord A exon
chr6:12229902-12230039
Coord C2 exon
chr6:12230040-12230242
Length
138 bp
Sequences
Splice sites
5' ss Seq
AAAGTGAGC
5' ss Score
5.89
3' ss Seq
AGTTTTGTATTACATCTTAGTTT
3' ss Score
4.37
Exon sequences
Seq C1 exon
TTGTCAGAACCGCCAGCTTAAAAGGTCGAAGAGGTCGCCTCCCCTCCAAACCTAAAAGTCCGCAGGATATCCCTGTCTCTTTCACACCCGTCAATCTCCTGAACGCACTAGTGAGAGCGCACATAGACTCCAACCCCTCCATGGCCCGTCTGGACTACTCTAAA
Seq A exon
GTGAGCTTCAAACTTCCAACATTCTGTAAAATAAATTTAAGTTTTAAGTCAAATTGACAATTTAATTATTGTTTTAGAATATGACCAAAATACATTTACTCTATTATATTCCATTAACAGTTTTGTATTACATCTTAG
Seq C2 exon
TTTCAGACGAGTCCGGAGTATCACAGTGGAGGAGATGAATCTCTGCACATTCAGCAGTTCTACGATCTACTCACTGCCTCAATGAGCATCATTCGCGGATGGGCCGAAAAAATCCCCGGCTTTACCGAGCTGCCCAAATGCGACCAGGAGCTCCTTTTCGAGTCTGCCTTCCTTGAACTCTTCGTGTTGCGGCTGGCGTACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000044532:ENSDART00000065385:5
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.226 A=NA C2=0.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0010425=Hormone_recep=PU(35.1=97.1)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CACCCGTCAATCTCCTGAACG
R:
GCAGACTCGAAAAGGAGCTCC
Band lengths:
247-385
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]