DreINT0123118 @ danRer10
Intron Retention
Gene
ENSDARG00000014101 | pyroxd2
Description
pyridine nucleotide-disulphide oxidoreductase domain 2 [Source:ZFIN;Acc:ZDB-GENE-050506-147]
Coordinates
chr13:40167583-40168129:-
Coord C1 exon
chr13:40167973-40168129
Coord A exon
chr13:40167738-40167972
Coord C2 exon
chr13:40167583-40167737
Length
235 bp
Sequences
Splice sites
5' ss Seq
CAGGTTAGC
5' ss Score
4.9
3' ss Seq
GTGTTTTGTTTTTGTTTCAGGCC
3' ss Score
11.46
Exon sequences
Seq C1 exon
TGGCTGTAGACAAGCTGCCAGATTTCTTGGCTGCTCCGAATGGCGCGGATGGAAAAGCGGGTCCTCATCATCAGTGTTCAATCCACCTGAACTGTGAGAGCGTGGAGGTGCTGGAAGACGCTTATTGGGAGGGTCAGCATGGTCGGCCATCCTCCAG
Seq A exon
GTTAGCAAAACCTGCAGCTCGGCTTATAATGGAACAACTAATATTTGCACATTACACACACATGAAGGCATCAGCACATCTGAATTTGCAAGTCATGACCTGAGTCACAGAAAGACAGCACATCTGTTGCTTGCAACCAGTGCTTATGCTAATGGCTTTCCATTCGTTGTACCAAACCACTGCGATTTACATGATAAGCCAATTCATCTTCTGGTGTGTTTTGTTTTTGTTTCAG
Seq C2 exon
GCCCATGATAGAAATGACCATTCCCTCAGTGCTGGATCCCACTCTAGCGCCGCCTGGATGTCACGTGGTGTCACTTTTTATACAGTTTACACCATATTTGCTTGAGGGTCGCCGTGCTTGGACTGATGAGGATAAGGAGAGGTTTGGGGACACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000014101:ENSDART00000144360:5
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.151 A=NA C2=0.094
Domain overlap (PFAM):
C1:
PF0159319=Amino_oxidase=PD(4.3=11.3)
A:
NA
C2:
PF0126619=DAO=FE(18.6=100)
Main Inclusion 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:
TGCCAGATTTCTTGGCTGCTC
R:
TGTGTCCCCAAACCTCTCCTT
Band lengths:
296-531
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]