DreINT0106148 @ danRer10
Intron Retention
Gene
ENSDARG00000017007 | nr4a2a
Description
nuclear receptor subfamily 4, group A, member 2a [Source:ZFIN;Acc:ZDB-GENE-990415-184]
Coordinates
chr9:5077835-5078947:-
Coord C1 exon
chr9:5078843-5078947
Coord A exon
chr9:5078701-5078842
Coord C2 exon
chr9:5077835-5078700
Length
142 bp
Sequences
Splice sites
5' ss Seq
AAGGTACTT
5' ss Score
8.4
3' ss Seq
TTTGTTTGTTTTAATTGCAGCCA
3' ss Score
7.93
Exon sequences
Seq C1 exon
AGGCAGAATCCAGAACTGATTCGTTTGTCGTGAACCCTGTATTAAATTTCACCTGATAATATCACCTACGCCGAGATCTGCTGAGGAACAGTCCGACGACTGAAG
Seq A exon
GTACTTACGTTGAAATCAATTTGCTAAGGTTGCATGCAAGCTGAAAACGTGTTATTAGGGGAATGCGTGTTTATTTTATTTATTGTTTTTTATGATTGTCTTTCTGTTTATTTATTTATTTTTTTGTTTGTTTTAATTGCAG
Seq C2 exon
CCATGCCCTGCGTCCAGGCTCAGTATGGCTCATCTCCGCAAGGCGCTAGTCCTGCGTCTCAGAGCTACAGTTACCACACAAGCGGAGAATACAGCTGCGATTTCCTCACGCCAGAGTTTGTGAAGTTCAGCATGGACTTGACCAATACCGAAATCACCGCCGCCACCACCTCTTTGCCCAGCTTCAGTACGTTCATGGACAACTACAATACCAGTTATGACGTGAAGCCGCCCTGTCTTTACCAAGTACCCCATTCTGGAGAGCAGTCGTCCATCAAAGTAGAGGACGTCCAGATGCACACATATCATCAGCAGAGCCATTTAGGCCCGCAGTCTGAGGAAATGATGGCCCACCCTGGGCCTATGTATTTCAAACCGTCCTCACCTCATGGTCCGGGACCGGCGAACTTCCAGGTTCAGCCCAATCACATGTGGGAGGACCCGGGCTCTCTGCACACTTTTCATCAGAACTATATGACCTCGCACATGATAGATCAGCGGAAGAACCCCGTGTCCAGGCTCTCCCTTTTCTCCTTCAAGCAATCTCCGCCCGGTACACCTGTTTCTAGTTGTCAGATGCGCTTTGATGGGCCTCTCCATGTGTCCATGCACGACAGTACCGGGGCGCACCGAACCCTGGACAGTCAGAGTTTCGCCGTGCCCAGTACCATCAGGAAGCAGGCGGGGATCGCTTTCACCCACTCACTTCAGCTCAGTCACGGCCATCAGCTGATGGACAGTCAGGTGCCGTCACCTCCGTCTCGGGGATCTCCATCTACCGAAGGTTTATGTGCGGTGTGTGGGGACAACGCGGCTTGTCAGCACTATGGAGTCCGAACTTGTGAAGGGTGCAAAGGATTTTTTAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000017007:ENSDART00000149268:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
5' UTR
No structure available
Features
Disorder rate (Iupred):
C1=NA A=NA C2=0.458
Domain overlap (PFAM):
C1:
NA
A:
NA
C2:
PF0010513=zf-C4=PU(38.6=9.4)
Main Inclusion Isoform:
NA
Main Skipping Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TTCGTTTGTCGTGAACCCTGT
R:
GGCGGTGATTTCGGTATTGGT
Band lengths:
247-389
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]