RnoINT0118325 @ rn6
Intron Retention
Gene
ENSRNOG00000004864 | Prpf40a
Description
pre-mRNA processing factor 40 homolog A [Source:RGD Symbol;Acc:1311401]
Coordinates
chr3:38689297-38689809:-
Coord C1 exon
chr3:38689693-38689809
Coord A exon
chr3:38689435-38689692
Coord C2 exon
chr3:38689297-38689434
Length
258 bp
Sequences
Splice sites
5' ss Seq
AGTGTAAGT
5' ss Score
8.46
3' ss Seq
TAGATTTGATTTTTTGATAGTTA
3' ss Score
2.61
Exon sequences
Seq C1 exon
GATAAAGGATTTGTAGTTGAAGTAAACACTACTTTTGAAGATTTTGTGGCAATAATCAGTTCAACCAAAAGATCAACCACTTTGGATGCTGGAAATATCAAGTTGGCTTTCAATAGT
Seq A exon
GTAAGTTAAATTATTGCACATATCTACCTTATCATCTAAAAATTACTTAAGGTTGTAGGCCAGTGGAATAAGATAGAGTAAATGGGATTTATAAGGTAAAGTAAAATAAAATGTATAAAGATTTTTCATTGTTAGAGGTCAAATCAAACTCTTATAAATGATATGATAATACTTTTAAGAACAATGGCTTATATGTTACTTTTAAACAGTGTTTGAAACAGGACTTATCATAACTTATTAGATTTGATTTTTTGATAG
Seq C2 exon
TTACTAGAAAAGGCAGAAGCCCGTGAACGTGAGAGAGAAAAGGAAGAAGCTCGGAAAATGAAACGAAAAGAGTCTGCCTTTAAGAGTATGTTGAAACAGGCCACTCCTCCAATAGAACTGGATGCTGTCTGGGAAGAT
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000004864:ENSRNOT00000006549:19
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=0.449
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0184614=FF=PU(46.2=52.2)
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:
AAGGATTTGTAGTTGAAGTAAACACT
R:
TCCCAGACAGCATCCAGTTCT
Band lengths:
247-505
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]