RnoINT0118324 @ rn6
Intron Retention
Gene
ENSRNOG00000004864 | Prpf40a
Description
pre-mRNA processing factor 40 homolog A [Source:RGD Symbol;Acc:1311401]
Coordinates
chr3:38689693-38689986:-
Coord C1 exon
chr3:38689895-38689986
Coord A exon
chr3:38689810-38689894
Coord C2 exon
chr3:38689693-38689809
Length
85 bp
Sequences
Splice sites
5' ss Seq
AAGGTAAAT
5' ss Score
8.88
3' ss Seq
ATAAGATTTCTGGCTTTTAGGAT
3' ss Score
7.53
Exon sequences
Seq C1 exon
GATCAACTGCACTTGATCTTTTCAAGTTTTATGTTGAAGATCTTAAAGCACGATATCATGATGAAAAAAAGATAATAAAAGACATTCTGAAG
Seq A exon
GTAAATAAATACTTGTTCTTAACTATTTGAAAACATTAATTCATTGCAGTCATGTGTTATTTATAATAAGATTTCTGGCTTTTAG
Seq C2 exon
GATAAAGGATTTGTAGTTGAAGTAAACACTACTTTTGAAGATTTTGTGGCAATAATCAGTTCAACCAAAAGATCAACCACTTTGGATGCTGGAAATATCAAGTTGGCTTTCAATAGT
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000004864:ENSRNOT00000006549:18
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=0.000
Domain overlap (PFAM):
C1:
PF0184614=FF=PD(17.9=32.3)
A:
NA
C2:
NO
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:
TCAACTGCACTTGATCTTTTCAA
R:
TCCAGCATCCAAAGTGGTTGA
Band lengths:
183-268
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]