DreINT0106109 @ danRer10
Intron Retention
Gene
ENSDARG00000045904 | nr2e3
Description
nuclear receptor subfamily 2, group E, member 3 [Source:ZFIN;Acc:ZDB-GENE-041114-63]
Coordinates
chr25:22177094-22177773:+
Coord C1 exon
chr25:22177094-22177483
Coord A exon
chr25:22177484-22177622
Coord C2 exon
chr25:22177623-22177773
Length
139 bp
Sequences
Splice sites
5' ss Seq
ACGGTGAGC
5' ss Score
9.44
3' ss Seq
TGTTTCTTGTGTTCCTCTAGGTA
3' ss Score
12.9
Exon sequences
Seq C1 exon
AGCCTCAGAGTCACTCACTGTCCGGCATCGCTAGACATACCAGGAGGAGGTGACAAACCTCCCTGCACTTTACAAAAGCTACAGACAAGAAGTTCTGCAGGACAGAGATACCCAGAGTCAAGAGCGGACCATCAGGATAGAGACTAAAGGATCTTGAAGAAACATCTAACAAGGAGTGACGGATCTCTTTGAGGACCCTCTAGGATTCTAGTTAACCTATCTGGGACACATATTCTAGCCTCAAAACTTTTGAGGGTGCACTTCAGGAAGAGTCTGCGTAAACTTTTACACCACCTTCAATGGAGGATCCGATGTCAGAAATGTCCATGGTACCGTTTTCATCACCAACAGAATCTTCCAGAAGCAACTCCACAGATGACAGCCAAGACG
Seq A exon
GTGAGCAACTTGTAAATTTACTTGTAAATCACTTTTAAAAGTTTCAGACAGCATAGGGTGACATATTAAGTCTGGTGATTATCAGATTCTAATCATTGGATTGGTAGTAAAACAAAAATTGTTTCTTGTGTTCCTCTAG
Seq C2 exon
GTAAAAGCCCAGCTCCTGGAAAGGTCCTGAACACGGGACTTCTTTGTAAAGTGTGTTCTGACACCAGCAGTGGGAAACACTATGGAATATACGCTTGCAACGGTTGCAGTGGCTTTTTCAAGCGCAGTGTGAGGCGCAGACTCATCTACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000045904:ENSDART00000127099:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=1.000 A=NA C2=0.098
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0010513=zf-C4=PU(52.1=72.5)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Rat
(rn6)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TGAGGGTGCACTTCAGGAAGA
R:
AAAAAGCCACTGCAACCGTTG
Band lengths:
258-397
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]