DreINT0106151 @ danRer10
Intron Retention
Gene
ENSDARG00000044532 | nr4a2b
Description
nuclear receptor subfamily 4, group A, member 2b [Source:ZFIN;Acc:ZDB-GENE-040718-103]
Coordinates
chr6:12228007-12229637:+
Coord C1 exon
chr6:12228007-12228857
Coord A exon
chr6:12228858-12229507
Coord C2 exon
chr6:12229508-12229637
Length
650 bp
Sequences
Splice sites
5' ss Seq
AAGGTAAAA
5' ss Score
8.38
3' ss Seq
CATGTGCTGTTTCTCCATAGCGC
3' ss Score
11.33
Exon sequences
Seq C1 exon
CCATGCCCTGCGTCCAGGCTCAGTATGGGACATCACCTCCAGGAGCCAGCCCTGCATCTCAGAGTTACAGCTACAACACCACGGGAGAGTACAACTGCGACTTCTTAACGCCGGAGTTTGTCAAGTTTAGCATGGACCTGACTAACGCAGAGATAGCTGTCACTTCTTCGCTCCCCAGTTTCAGCACCTTCGTGGACACCTACAACTCCAACTACGACGTGAAGCCTCCCTGCCTCTACCAAATGGCCCACTCTGGGGATCAGCTGTCCATCAAGGTGGAGGAGATACCCGCACACGGCTACCATCAGCAGCAGCACCATCAGCCGCATCAGGCTGAGGAGAGCATACCCCATACCGGAGCTATATACTATAAACCATCCACTCCAAACATCTCCCAGTCCCCCAGTTACCCAACGGCTCCACATCATACGTGGGAAGACACCGGATCCCTTCACAGCTTTCACCAGAACTACCTGGCGACGTCACATATTATGGACCAGCAGCGGAAAAACGCGATGTCTCGGTTATTCTCGTTCAAGCAGTCTCCGGTTGACACGCCGATGCCAAGCTGCCAGATGCGCTTCGATGGATCCCTGCACGTGTCCATGGGCCCGGACACCGCACATCGCGCGCTGGACAGTTTTGCTTTGCCGGCTCCTCCGAGGAAACAGCACGGTGTGGGTTTATCCCATTCCCTAAACGTCGGGCACCCCTTACTGGAAAGCCCGGTGGCATCACCGCAGGCTAGAGGATCTCCGTCCAGCGAGGGTTTGTGCGCTGTGTGCGGGGACAACGCAGCCTGTCAGCACTACGGAGTGCGCACATGCGAGGGGTGCAAAGGATTCTTTAAG
Seq A exon
GTAAAAATTAGCCAATGACCACAAATCTTTTATTCAAAGTACATTTATTATGGGCCCTCGGCACTTGTTTTTTGCATGGAAATGACTGTAGTTCATGGTTCACCCTTTGCAGTCAGGGTCTGAACCTATAACCTTATGTTGCCAACCCTACTAGAGATTGGAACACAGTTTAGGACTGGTCTGGTACACACAGTATTCCCTTATTTATCTCAGTTGTATTGATTTGACCCGATGTGCACCCAGGGACACCTCCGCTCATCTCCGCCACTATTACGCTCGTCCAGAATTAAATTGGTTTGTGCTTAGAGTCGTATTGCGCCTAACCGTGCGTAACGGAACTCCCAGTGGTGACATTAAGACAGCTCTTTATGTCACCCTCGTGATAGAATAATCTCACTAATCCGACAAGAGGGGTCGCCGAGAGAGCGCCGGGGGACCCCAAATTATGACTGCCCACGGATCTGTATTTACCGAATGTCTGCCCTGTCCGGCCCTTGAATGTATTACACAGCTTTGGGTTGGAGTGCAGGGTTTGAGTGTCCTATTCTATTGTGATCTCACATTGTGATTGCAGTTCAAGTTGTTTCTGTGCGAATGGAGTTGATTTACATGCAATTAATACACATCATACATGTGCTGTTTCTCCATAG
Seq C2 exon
CGCACGGTGCAGAAAAACGCCAAATACGTTTGTCTGGCGAACAAAAACTGTCCTGTGGACAAAAGACGGCGAAATCGATGCCAATATTGCCGTTTTCAAAAGTGCCTGGTCGTTGGGATGGTAAAGGAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000044532:ENSDART00000065385:3
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.403 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0010513=zf-C4=PU(38.6=9.5)
A:
NA
C2:
PF0010513=zf-C4=PD(58.6=93.2)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CAGATGCGCTTCGATGGATCC
R:
TTTCGCCGTCTTTTGTCCACA
Band lengths:
353-1003
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]