DreINT0119311 @ danRer10
Intron Retention
Gene
ENSDARG00000006288 | prdm5
Description
PR domain containing 5 [Source:ZFIN;Acc:ZDB-GENE-040708-1]
Coordinates
chr23:2011145-2011753:-
Coord C1 exon
chr23:2011576-2011753
Coord A exon
chr23:2011241-2011575
Coord C2 exon
chr23:2011145-2011240
Length
335 bp
Sequences
Splice sites
5' ss Seq
CCAGTCAGT
5' ss Score
0.29
3' ss Seq
GTGTGTGTGTGTGTGTGTAGTCT
3' ss Score
7.24
Exon sequences
Seq C1 exon
AGCTGATGATCAAAAAGGAGGATTACCCATGTCTGCTGTGCGAGAGCAGCTTCCCCAGTGAAGACGTGCTAGCAGAGCATCTCCAGAGCCTCCACAACAGAGGAAGTGCTGAAGACAAAGAGTTTAAGTGTCGATCCTGCGGAAAAGAGTTTCCCGTCAGACAAGCCCTGCAGCGCCA
Seq A exon
GTCAGTACCACACACACACACATACACGCAAACAAACACACGCAAACATACATATATACATGCATACAGTATGTACAACAAGCATACATAAACACACACATGCACACTCAGTGTCATGTGCTGTAATGCTTACTCGCTCAAACACACAGAAACAATCACACAAACACAAACAAATACACACACACACACACAGACACACACACACACACACTAACAAACACAATTTTATTCTCATACACGCAATCACTTTCGCACACAAATGCACACAGACTCACACAGCACACAAACAGTAATGCTGATGTCCTGTGTGTGTGTGTGTGTGTGTGTGTGTGTAG
Seq C2 exon
TCTCCTTCACTGTACAGAGAGCTCTTCTTCATCAGGAGACCCTTCTAAAGCTTATCAGTGTGTCCTGTGTCACGGCTCCTTCAGCTCACAGTCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000006288:ENSDART00000127443:5
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.067 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0389611=TRAP_alpha=FE(42.4=100),PF138941=zf-C2H2_4=WD(100=40.0),PF097235=Zn-ribbon_8=PU(59.4=31.7),PF0009621=zf-C2H2=PU(78.3=30.0)
A:
NA
C2:
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)
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:
AGCTGATGATCAAAAAGGAGGA
R:
CTGGACTGTGAGCTGAAGGAG
Band lengths:
274-609
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]