RnoALTD0023656-2/4 @ rn6
Alternative 5'ss
Gene
ENSRNOG00000004864 | Prpf40a
Description
pre-mRNA processing factor 40 homolog A [Source:RGD Symbol;Acc:1311401]
Coordinates
chr3:38739889-38741175:-
Coord C1 exon
chr3:38741075-38741175
Coord A exon
chr3:38740949-38741074
Coord C2 exon
chr3:38739889-38740020
Length
126 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
GATCGCTTCTTGTTGGTATGTGTAGCGGCAGTGGCCGCCGACGGAGCAGTCTGAGCCCGACGATGAGGCCGGGGACTGGAGCCGAGCGTGGAGGCCTCATG
Seq A exon
GTGAGTGAAATGGAGAGCCAACCTCCCTCGCGGGGTCCCGGGGACGGGGAGCGGAGATTGTCCGGCTCAAACCTGTGCTCCAGTTCTTGGGTCTCTGCTGACGGCTTCCTGAGGAGACGGCCCTCG
Seq C2 exon
ATGGGGCATCCTGGCATGCATTATGCACCAATGGGCATGCACCCTATGGGTCAGCGAGCAAACATGCCTCCTGTACCTCACGGAATGATGCCACAGATGATGCCTCCTATGGGAGGGCCTCCAATGGGACAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000004864-0-0,1-0,2-0,3-0-2/4
Average complexity
Alt5
Mappability confidence:
NA
Protein Impact
Protein isoform when splice site is used (Ref)
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 Skipping Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Human
(hg19)
No conservation detected
Mouse
(mm9)
No conservation detected
Cow
(bosTau6)
No conservation detected
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TCTTGTTGGTATGTGTAGCGGC
R:
TTGTCCCATTGGAGGCCCTC
Band lengths:
226-352
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]