DreINT0120519 @ danRer10
Intron Retention
Gene
ENSDARG00000058467 | prpf40a
Description
PRP40 pre-mRNA processing factor 40 homolog A (S. cerevisiae) [Source:ZFIN;Acc:ZDB-GENE-030131-274]
Coordinates
chr9:4730904-4731243:+
Coord C1 exon
chr9:4730904-4730968
Coord A exon
chr9:4730969-4731078
Coord C2 exon
chr9:4731079-4731243
Length
110 bp
Sequences
Splice sites
5' ss Seq
CAGGTATCC
5' ss Score
7.91
3' ss Seq
CTTTCTCTGTGTGTGTGCAGTGC
3' ss Score
9.59
Exon sequences
Seq C1 exon
GGCGTTTCTTCCAATGCATCATGGGAGCAGGCAATGAAGCTGATAATTAATGACCCTCGTTACAG
Seq A exon
GTATCCAAATACTGCACAGCATTATTGGCATTTATTAGCGTTTACATCCTGCGCCGTTAAACAAATTTGTGCGATTCTTCACTGACGTCCCTTTCTCTGTGTGTGTGCAG
Seq C2 exon
TGCTCTGCCAAAGCTCAGTGAGAAGAAACAGGCGTTCAATGCTTATAAAGTCCAGACAGAGAAAGAGGAAAAGGAAGAAGCCAGAATAAAATACAAGGAGTCTAAAGAGACTTTCCAACGCTTCCTGGAGAACCACGAGAAGATGACGTCAACCACACGATACAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000058467:ENSDART00000081326:12
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=0.268
Domain overlap (PFAM):
C1:
PF0184614=FF=FE(42.0=100)
A:
NA
C2:
PF0184614=FF=PD(30.0=26.8),PF0184614=FF=PU(44.0=39.3)
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:
GGCGTTTCTTCCAATGCATCA
R:
ATCGTGTGGTTGACGTCATCT
Band lengths:
226-336
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]