DreINT0119312 @ danRer10
Intron Retention
Gene
ENSDARG00000006288 | prdm5
Description
PR domain containing 5 [Source:ZFIN;Acc:ZDB-GENE-040708-1]
Coordinates
chr23:2010912-2011240:-
Coord C1 exon
chr23:2011145-2011240
Coord A exon
chr23:2011034-2011144
Coord C2 exon
chr23:2010912-2011033
Length
111 bp
Sequences
Splice sites
5' ss Seq
CAGGTACTG
5' ss Score
9.04
3' ss Seq
AGTTGTGTGTGTGTGTTCAGTTT
3' ss Score
6.86
Exon sequences
Seq C1 exon
TCTCCTTCACTGTACAGAGAGCTCTTCTTCATCAGGAGACCCTTCTAAAGCTTATCAGTGTGTCCTGTGTCACGGCTCCTTCAGCTCACAGTCCAG
Seq A exon
GTACTGCACTCCTGCGTGTCATATGGATGTGTGTCTCATGACAAGAGCAAGACGAAATGCAGACAGCATTGTGAGTTGATTTGAATCCAGAAGTTGTGTGTGTGTGTTCAG
Seq C2 exon
TTTCCTGCAGCATAAAGAGGCGTGTAAAGGAGACGAACGCTTCATCTGTAAGGCGGAGAGCTGTGGGAAGAGATTCAAGAGTAAAGACGCACTCAAGAAACACAAAGGCAACATCCATATAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000006288:ENSDART00000127443:6
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.024
Domain overlap (PFAM):
C1:
PF0389611=TRAP_alpha=PD(10.1=42.4),PF097235=Zn-ribbon_8=PD(37.5=36.4),PF0009621=zf-C2H2=PD(17.4=12.1)
A:
NA
C2:
PF0009621=zf-C2H2=WD(100=61.9)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TCTCCTTCACTGTACAGAGAGCT
R:
CTATATGGATGTTGCCTTTGTGTT
Band lengths:
218-329
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]