RnoINT0118335 @ rn6
Intron Retention
Gene
ENSRNOG00000004864 | Prpf40a
Description
pre-mRNA processing factor 40 homolog A [Source:RGD Symbol;Acc:1311401]
Coordinates
chr3:38703543-38706000:-
Coord C1 exon
chr3:38705890-38706000
Coord A exon
chr3:38703664-38705889
Coord C2 exon
chr3:38703543-38703663
Length
2226 bp
Sequences
Splice sites
5' ss Seq
GAGGTAAAT
5' ss Score
8.39
3' ss Seq
GAGTGTTTTCCCTTCTTTAGCAA
3' ss Score
6.7
Exon sequences
Seq C1 exon
AAATCAATGTGGACAGAACATAAATCACCTGATGGAAGGACTTATTACTATAATACTGAAACAAAACAGTCTACCTGGGAAAAGCCAGATGATCTTAAAACACCTGCTGAG
Seq A exon
GTAAATGTTTGAACACTAGGAATCAGAACTGTTAATTAGCTTGGGTATATTTCTTAGAATTTATATTAAGCTCCAAAGAGCAGTTCTTCTGTGTCTCTATTTAGTTAAGACATTGGGTGAAGAGGTTTACTGTAGTTAGAATAGTCAGCAAGAGTAAAATTTGTTCTCCTATATGGACATACTTTTTTTTATTATCATCCTATATTCAAAGTTGTCAAGAGTAAGTTGAAGGGTAAAGCAGTTTTCTTCAATATAGTATGACCTGTATGATTTTAAAAAACATGTTAGCAGTTCCAGTTAACCATGGAGTTTGATATAATGAAATTAAATAACCTACAAAATACTTTCTTGTCTTAGAATATTTTCTCTTTGTAGACATACCTCTGAAAGGGTATTATTTTGTGTTATACACTTCGACATTCAAAATAGATAAATGTGACAAAATTAAGAGTGAAACAATAAATTAAGCAATATTGCATTTTTTAATAGTCATGCTCAGAAAGAGGTGATCTTTTTCACTGAAGAATGTTTCACCTAGCCAGTGGTATTCCGTTTTCATTTTCCTTAACTAAAGTACTCAAGACAGTAAATAAATGTATTTTCCACACATTGTATTACCCCTGTATCTAATATGAAGATAGTGTTTGAGAAGGAAGGTTAATAGATAACATTTATTTCTCATTCATATACACACACTTTCGGGCTTATAGCAAATTAATTTGAAACTAAAACATTAGGATGGATGAGTCAGATTTCACCTCTCCCCAAACTTTCTGTTTGTCTATTTGTACTAATATATGAATATTCCATTTACTAATTATGGGTGGTGGTTTTTACCTATGGTGAACATAAGAGGGGGTGTACACACAGTTAAAATTCAGGTAGATGCCTAACTTTGAGGAAGCATCCCTGCACTTCTTAAGTATATTATTTCTAACAAATTATTTTCCTTTCAAAAGTTAAATGATTTATTCAATAGTCAACAACTCTTATTTTTTTTTAATTACATTTCAAATGTCATTCCCTTTCCTGGTTTCCCGGACATAAGCCCCCTCTCCCACCCCTCTTCCCTTCTTCTATAAGGGTGTTCGCCCTCCCCAACCAACCTCCCTTCCATCCCCCTTGACATTCCCCTGTACTGGGGGTTCCAGCCTTGGCAGGACCAAGGGCTTCTCCTCCCATTGGTGCCCAACAAGGCCATCCTCTGCTACATATCAGTGGGAGCCATGGATCAGTCCATGTGTACTCTTTGGATGGTGGTTTAGTCTTTGGGAGCTCTGGTTGGTTGGTATTGCTGTTCTTATGGGGTTGGAAAACCCTTCAGCTCCTTCAATCCTTTCTCTAACTCCTCCAACGGGGACCCCATTCTCAGTTCACCTCTATATTTGACATGCTCTGGCTGAGCCTCTCTCAGGAGATAGCTATATCCAGCTCCTGTCAGCATGCACTTCTTGACTTCATCAATATTACCTAGTTTTGGTGGCTGTACATATATGGGCTATATACCCAGGTGGAGCAGGATCTGAATGGCCATTCCTTTCAGTCTCTGCTCCAAACTTTGTCTCCATATCCCCTCTTATGGATATTTTTGTTCCCCCATTTAAGATGGACTGAAACATCCTCACTGGTCATCCTTCTTGAGCTTCATGTGGTCTGTGGATTGTATCTATGGTAATTCAAGCTTTTGGGCTAATATCCACTTAATCAATGAGTGCATACCATGTGTGGTTTGCTGTGATTGGGTTACCTCACTCAGGATAATATTTTCTAGTTCTATCCATTTGCCTGTAAGTTTCATGAAGTCATTGTTTTTGATAGCTGAGTAGTATTCCATTGTGTAGATGTACCACATTTTCTGTATTCATTCCTCAGTTGAGGGACATCTGGGTTCTTTCCAGCTTCTGGCTATTATAAATAAGGCTGCTATGAACATAGTGGAGCATGTGTCCTTGTTGTATGTTGGGGCATCATTTGGGTATATGCCCAGGAGAGGTATAGCTGGGTCCTCAGGTAGTGCAATGTCCAATTTTCTGAGGAACCTCCAGACTGATTTTCAGGAGTGGTTGTACCAGTTTGCAATCCCACCAACAATGGAGGAGTGTTCCTCTTTCATGCTATGAATGTATATTGAGTTACGTGGGTAGACAATGTCTAGTGAAAACAAGTGTGAATTGTCAGCAATGTTGAGCATGTTATTATTTGCTGAGAGTGTTTTCCCTTCTTTAG
Seq C2 exon
CAACTATTGTCTAAATGCCCATGGAAAGAGTACAAATCTGATTCTGGGAAGCCTTATTACTATAATTCTCAAACAAAAGAGTCCCGCTGGGCCAAACCTAAGGAACTTGAAGATCTTGAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000004864:ENSRNOT00000006549:6
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.791 A=NA C2=0.585
Domain overlap (PFAM):
C1:
PF0039721=WW=PD(93.3=75.7)
A:
NA
C2:
PF0039721=WW=WD(100=73.2)
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:
No suggested primer sequences
R:
No suggested primer sequences
Band lengths:
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]