GgaINT0068810 @ galGal4
Intron Retention
Gene
ENSGALG00000011963 | PRDM5
Description
PR domain containing 5 [Source:HGNC Symbol;Acc:HGNC:9349]
Coordinates
chr4:53677232-53677707:+
Coord C1 exon
chr4:53677232-53677324
Coord A exon
chr4:53677325-53677585
Coord C2 exon
chr4:53677586-53677707
Length
261 bp
Sequences
Splice sites
5' ss Seq
GAGGTTTTG
5' ss Score
-0.23
3' ss Seq
TTGCTGATTATCCCATATAGTTA
3' ss Score
4.01
Exon sequences
Seq C1 exon
TGTACTTCAGTGCACAGAGAATATCAACCCAGGAGACTCTTCAAGAAGTTTTCAGTGTTCTGTTTGCAATACTTCCTTCAGCTCAGAATCGAG
Seq A exon
GTTTTGTGTCCGAGTTACTGGACTGCTGTCATACCATTGCTGGCCTTCCTTTGCATGTTAGCTTTCAAGCTTGTTAGTGTATGTGAATCCTAACAATGAAAGAAGTCAAATGCTTTCATTCTTATTTGCTGTAAGTAATGCATGAGGTGGCCTTGGAACTCTGCAGTGCAGCACGTGTAAAGCTCAGAGTACTTACTATATGTCTGATTTCTGCATACACTGCGTCATGTGTTATTTTTATTTGCTGATTATCCCATATAG
Seq C2 exon
TTATGAACAGCACAAGGAGGCATGCAGAGGGGATGCCAGATTCATATGCAAGGCAGATAGCTGCGGGAAGAGGTTCAAGAGTAAGGATGCCCTGAAAAAACATAAGGAAAATGTTCATAGTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000011963:ENSGALT00000019510:6
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=0.167
Domain overlap (PFAM):
C1:
PF0009621=zf-C2H2=PD(17.4=12.5),PF128742=zf-met=PU(66.7=43.8)
A:
NA
C2:
PF128742=zf-met=PD(28.6=14.3),PF0009621=zf-C2H2=WD(100=61.9)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TGTACTTCAGTGCACAGAGAAT
R:
TCAGGGCATCCTTACTCTTGA
Band lengths:
188-449
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]