DreINT0106155 @ danRer10
Intron Retention
Gene
ENSDARG00000044532 | nr4a2b
Description
nuclear receptor subfamily 4, group A, member 2b [Source:ZFIN;Acc:ZDB-GENE-040718-103]
Coordinates
chr6:12230324-12231692:+
Coord C1 exon
chr6:12230324-12230502
Coord A exon
chr6:12230503-12230588
Coord C2 exon
chr6:12230589-12231692
Length
86 bp
Sequences
Splice sites
5' ss Seq
CAGGTAAGA
5' ss Score
10.77
3' ss Seq
GTTTTTTCTTATCTCCATAGAGA
3' ss Score
10.28
Exon sequences
Seq C1 exon
ATCTAACCTGCCAGAGGACAAACTCATCTTTTGCAACGGAATGGTTTTACACAAGTTGCAGTGCGTGCGAGGCTTTGGGGAGTGGATCGACTCTATTGTCGAGTTTTCTTCTAATCTTCAGAGCATGAGCTTAGACGTGTCTGCCTTCTCCTGCATAGCCGCTCTCACCATAGTAACAG
Seq A exon
GTAAGACATGTCTGACCTTTTCCAAGTGATGCACAGAATATACAGCATGTTTCAGAGCTCTGACGGGTTTTTTCTTATCTCCATAG
Seq C2 exon
AGAGACACGGACTAAAGGAGCCCAAGAAAGCAGAGGAACTTCAAAACAAGCTCATAAACTGTCTGAAGGATCAGGTGTCCTGCAGTGGTGAATTGTCTAAACTGTTGGAGAAGCTGCCGGAGGTGCGCGCGCTGTGCACGCAGGGTCTGCAGCGCATCTTTTACTTGAAACTGGAGGATTTGGTGCCCACGCCTGCGATCATTGATAAACTCTTTCATGACACTTTACCATTCTAAACAATCTCGTCTGAACTGAAGCAGGTTCTCGAAACCTTGTTATTCTTCGATGTTGCGGACTTTTTAGGAAATGAAAATGGCGGATGGTATTTTTAAAGATCGGAGAAAGACTGCCCGGGACAAAACTGAACAGTCCTATTTGGAGGAAATAATTATTCAAGAAAAATATTATGGAGGAAAAGGGACTATTCTTATGCCTGTTTAAAGTGTATTCAGTTATATACTGAAAATAAATGCGGTGTGGTGGACATGTATTTGTATTGTTACGCGTCATATTGTTTATGTTACCTGCAAAGCATTTATATACACCTTTACACGTGTCATCAAGATGTAGCCTAATGATTTAAGGGATCAAAATAATTTTGACAAGGTACTTTACTAATTAAGTCATTCTGCATTATAGTCTATAGAGATTGCACTGAGAGTGCACGAGATAATTCTTAAAACTCTATCTGCAACATTTCAGATTTCAGAATAGATACAAACAAATAAAGCACGTTTTTGTGTTTATGATTTTAAAGTAGTGAATTATACTGTTATTAAGATATGGGTCGCTTTTTTACTGTCCAGAAAGTATGCATGAAGGGAATTCGTTATGAGCTATTAACTTTCTCCAGCACTTTGTATTAATTTCATATTGAAATAACGTCCATGAGGTTTACGTGCAACTGGTTTAAAATTCTTACATTATGCTTATATTTCTCAGATCATTGTTTTCTATATGATGTTATGGATTTTGCACTGCATTCTATGTTAAGCTTCTCTCATCTAGTGTATTGCTGAATAAACCTAACTATTATATATTTCCTCTTGTTTGTTTGTCAGTAACATTTACTTTCGATGCATATTAAAATTTCCAGATTGTTTA
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000044532:ENSDART00000065385:7
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0010425=Hormone_recep=FE(31.9=100)
A:
NA
C2:
PF0010425=Hormone_recep=PD(32.4=77.2)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TGAGCTTAGACGTGTCTGCCT
R:
CGGCAGCTTCTCCAACAGTTT
Band lengths:
173-259
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]