GgaINT0068809 @ galGal3
Intron Retention
Gene
ENSGALG00000011963 | PRDM5
Description
NA
Coordinates
chr4:55802191-55803629:+
Coord C1 exon
chr4:55802191-55802365
Coord A exon
chr4:55802366-55803536
Coord C2 exon
chr4:55803537-55803629
Length
1171 bp
Sequences
Splice sites
5' ss Seq
ACAGTGAGT
5' ss Score
8.34
3' ss Seq
TTATTTTTCTTTTTATTTAGTGT
3' ss Score
9.14
Exon sequences
Seq C1 exon
ATCCCCTCACTTGTAAAGAGGACCATGCATGCCCAAACTGTGAGTCCAGTTTTGCAAGCCAGGAGATTCTAGCTGAACATCTTCAGACATTGCACCAAAAACCCAGTGAGGAAAAAGAATTCAAGTGCCGAAACTGTGGAAAGAAATTCCCTGTTAAACAAGCTCTACAAAGACA
Seq A exon
GTGAGTAGAAACAAGAATGTTTTTCAGAGTTCCTTTTCATTCAATCATTTAATTTTTATTCTTTTTTATTTGTATCCTCACTCTTCTAATAAATTCTTAATATGTTAGTTTCCTGTATTTGTTGGAGACTTCAATTTGAATTAAAAATGTCACTAATTTTTAATATTTTCAAAACATATACTGTAAGTCCGATTAAAGCTACTGAGTGGTGCAGAGCCCTTCATCTCCATCTCGAGTGGGTTATTTAATAGTTTAAGAGATCTGTTTTAGCTGGAATTGCCACTACTGAATTAGAATGAGATTTAGAAAAAAAAATGAATGATATTCTAAAAAGAAATAGAAAGGAAAAGCCATACTTTATTTTGAATTAATTAAATATTTGGATTAAAAAAAACAAACAAACCATAAAAGATAGCAGATTTAAGAGTGTGTCTCGTTATTCTATCCTTGGTAGTATAAAAATGCAGTTTTGTCACTAAAGTCATGTGTCTTACATTATGTTTTTATACAAAAATATCAACATTTTCTTCTTTTCTTGTTTAGGTATATATATTTGCCTGCAATTAAATAGATATATTCCTTTTTATTATACATTTAATTATAGGTAGTATACTGGATGTCCAAATATCTTCTTATAAGTAGTACATTTAATCCAACTCTTGCATGTCAGAAAGAGACTCATGTTGCGTTGTGTATTACAACACTCCTCTTGTAATAAATTGGTTTTTCTTGTGTCTGAATAGCAATAATGTTTCTTAAATTGGCAGTTCTTTATGAGCTCTATGTTCTTTCATGGAAATAGATAAAAAAAAAATAGTAGAGAAATATTTGGTGGAGATAATTAAATATTTTTTATTGAACATTGACATGTTTCTTCTAGTCTGAATTGGGAGCTGGATTTGTGTTGTACAGCCGGTTAAGTGAATATGTTATGCAGTAATATGAAAAGTAAAAAACATTATGCAGTAAAATTAATCAGGATACAGCAATAAGACCACAACTCTTCATGTTCATGCACTTGATTAGTCCCACTAAATTTCAGGGCACCTCAGATGTTGCATTGGTTATTCATATATTGAAATGTTTGTATTTTGATCTATTGCTACTTCAATTCTGCGTAAGTTGTAAAATGGTCACCTTATTTTTATTTTTTATTTTTCTTTTTATTTAG
Seq C2 exon
TGTACTTCAGTGCACAGAGAATATCAACCCAGGAGACTCTTCAAGAAGTTTTCAGTGTTCTGTTTGCAATACTTCCTTCAGCTCAGAATCGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000011963:ENSGALT00000019510:5
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.085 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0396611=Trm112p=PD(70.7=89.8),PF0009621=zf-C2H2=PU(78.3=30.5)
A:
NA
C2:
PF0009621=zf-C2H2=PD(17.4=12.5),PF128742=zf-met=PU(66.7=43.8)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CCCCTCACTTGTAAAGAGGACC
R:
TCGATTCTGAGCTGAAGGAAGT
Band lengths:
265-1436
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]