DreINT0053694 @ danRer10
Intron Retention
Gene
ENSDARG00000025311 | cuzd1.2
Description
CUB and zona pellucida-like domains 1, tandem duplicate 2 [Source:ZFIN;Acc:ZDB-GENE-131119-30]
Coordinates
chr17:21822003-21822299:-
Coord C1 exon
chr17:21822237-21822299
Coord A exon
chr17:21822148-21822236
Coord C2 exon
chr17:21822003-21822147
Length
89 bp
Sequences
Splice sites
5' ss Seq
TGGGTAAGA
5' ss Score
8.91
3' ss Seq
TGTTTTTCCATCACATTCAGAAC
3' ss Score
7.92
Exon sequences
Seq C1 exon
TATGAAATATGGAAGCTCTCACTCTCCTTCTTTGTTTGCTTCTAACTACTAAGGCCTCTCTGG
Seq A exon
GTAAGAATCTAATTGTCTGTCTGTCTGTCTGAACAATTTTATACATATTGTATTGTCTTGTTGCCCTCTTGTTTTTCCATCACATTCAG
Seq C2 exon
AACCGTGTGGAGGATCCTTGAGTAGCTGGATGGGTGAATTTACTAGCCCCAATTACCCTAATAGTTACCCTGATAAAGCACGGTGCACATGGACCATTCACAGCACAGGGGCGGCAACTGTGTCACTGACCTTCACAGATGTTTT
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000025311:ENSDART00000154927:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0043115=CUB=PU(43.8=93.9)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Cow
(bosTau6)
No conservation detected
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AGCTCTCACTCTCCTTCTTTGT
R:
AAGGTCAGTGACACAGTTGCC
Band lengths:
183-272
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]