RnoINT0118315 @ rn6
Intron Retention
Gene
ENSRNOG00000004864 | Prpf40a
Description
pre-mRNA processing factor 40 homolog A [Source:RGD Symbol;Acc:1311401]
Coordinates
chr3:38739889-38741113:-
Coord C1 exon
chr3:38740949-38741113
Coord A exon
chr3:38740021-38740948
Coord C2 exon
chr3:38739889-38740020
Length
928 bp
Sequences
Splice sites
5' ss Seq
TCGGTAAGG
5' ss Score
10.48
3' ss Seq
TACTTTTCATTGTTTTTCAGATG
3' ss Score
10.36
Exon sequences
Seq C1 exon
ATGAGGCCGGGGACTGGAGCCGAGCGTGGAGGCCTCATGGTGAGTGAAATGGAGAGCCAACCTCCCTCGCGGGGTCCCGGGGACGGGGAGCGGAGATTGTCCGGCTCAAACCTGTGCTCCAGTTCTTGGGTCTCTGCTGACGGCTTCCTGAGGAGACGGCCCTCG
Seq A exon
GTAAGGGATCGGCGGGGTAGGGGAAAGCGGCACAATGAAAAACCGAGTCAGAGAAACAGGAAGCTTTCTCCAAAAGGAGACGAGTATACCAGGAAGAGAGCTCCAGATGGTGGGCTACGTCCCAAGGGAGAGAAATAGAGGGCGGGAACGCACAAAGAAATATGTGGGACCTTGGACTTGCCAGTGGTCTTGGCCTAAGTAGATGCCTTAGGAAGGGAGGTGCTGGGCCCCGGGCGGACTGCACGTCTGAAAGCCCCAGGCTTGCTTTATGGTAGGGAGAGGCTGCTGCAGTTTATTTTCCTCCGGAGTAGTGGTGATTTGCACCGGTTGGGGGATTTGGTTGGGAGAATTGGCTGCGGATACTTAGTTTCAAGCCAGGAACAATGGAAGTACTATATTTTTAGCTCACTAAAATGGATGAATTTGTTATTTGCATTTAGTGTCTGGGACAGAATGACAGTCTTTGATATTTTAACTATATTAAGACATTCGTTCCTTAACGAAGTACTCTTGGGTACCCACTCTGTTTTATGATCAGACCTCGTCCAAATTAATGTAATTTTAAGTAGTATAAACAGAGTATATGTATAAAGGTGACAAGGTTGGGTTCACCGTAATAATTTTAAGTTAGAATTCAATACATAGACACCAAGTCTGGCCAGTCATTTGACAGTTGGCTAAGTCATCGGAGAGGGATTTTAATCCGCTATTGGGATTAACTTCCCCATATTTTGTAAATTTTGAGGTTCCTCATAATAACCACTGTAGTATATTTTAGATTAACGTTACTAGATGCTAATCCTGTAGTTTAATCACATTGACTTAGTTGACTTTCAGTTCAGTTGATGGGTTTTAGTCGTTGTTTTTGAAATGACAGTTTAAAGAAACATTGATTGTGTCTTACCTCTTACTTTTCATTGTTTTTCAG
Seq C2 exon
ATGGGGCATCCTGGCATGCATTATGCACCAATGGGCATGCACCCTATGGGTCAGCGAGCAAACATGCCTCCTGTACCTCACGGAATGATGCCACAGATGATGCCTCCTATGGGAGGGCCTCCAATGGGACAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000004864:ENSRNOT00000006549:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.938 A=NA C2=0.991
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GACTGGAGCCGAGCGTGG
R:
TTGTCCCATTGGAGGCCCTC
Band lengths:
286-1214
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]