RnoALTD0005160-3/3 @ rn6
Alternative 5'ss
Gene
ENSRNOG00000020935 | Capn1
Description
calpain 1 [Source:RGD Symbol;Acc:2267]
Coordinates
chr1:221369333-221371252:-
Coord C1 exon
chr1:221371152-221371252
Coord A exon
chr1:221370837-221371151
Coord C2 exon
chr1:221369333-221369600
Length
315 bp
Sequences
Splice sites
5' ss Seq
GAGGTAAAC
5' ss Score
7.2
3' ss Seq
CAGGCCCATGTGTCCCCCAGGAT
3' ss Score
6.9
Exon sequences
Seq C1 exon
CTCTTGTGCGCCCAGGGGAATCTGGTGGGCCTGCCCTGATGTTCAGGGCCTCTGCTGCCCTCTCCCGGGTCAGGTGATCCCCACAAGGGCGCTGATTCCAG
Seq A exon
GTGGGTAGACCAAGAACTTGAGAAAAAAGGTCAGAATGCTACACAAAATTGTCCCTCTTTTTCTTTTGCATGGTTGGGGAAATCAAGGCACGGATTTACCTAAGGCCATGCAGGGAATGCGCAAAGACCGCTAGGGCGGAGTGCTAGCTCTGTAGGCCTGCGCCCTAAGGTGAGGGGGTGGGGAGCTGGCTCAGTCCTACAACCGGGATGCCGCAGGGACCGGCCGGGGTGGGGCTACCGTTTGTCTAGCGTCCGGCAGAAGTCCGTTCTCATCCAGCCAGGGGCGGCTTCAGCAAGCAGTTGGGGCAGCTAGAG
Seq C2 exon
GATGGCAGAGGAGTTAATCACACCTGTGTACTGCACCGGGGTGTCAGCCCAAGTGCAGAAGCAACGGGACAAGGAGTTGGGCTTGGGCCGCCATGAAAATGCCATCAAGTACCTGGGCCAGGATTATGAAAATCTTCGTGCAAGATGCCTGCAGAACGGGGTCCTCTTCCAAGACGATGCCTTCCCTCCAGTTTCTCATAGCTTGGGCTTCAAGGAACTGGGTCCCAATTCCTCTAAAACCTATGGCATCAAGTGGAAGCGTCCTACG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000020935-0-2,1-2,2-2-3/3
Average complexity
Alt5
Mappability confidence:
NA
Protein Impact
In the CDS, with uncertain impact
No structure available
Features
Disorder rate (Iupred):
C1=NA A=NA C2=0.022
Domain overlap (PFAM):
C1:
NA
A:
NA
C2:
PF0064816=Peptidase_C2=PU(11.3=38.2)
Main Inclusion Isoform:
NA
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:
GGCCTGCCCTGATGTTCAG
R:
CGTAGGACGCTTCCACTTGAT
Band lengths:
342-657
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]