RnoALTD0027024-2/2 @ rn6
Alternative 5'ss
Gene
ENSRNOG00000021101 | Sema6c
Description
semaphorin 6C [Source:RGD Symbol;Acc:3659]
Coordinates
chr2:196337997-196338453:+
Coord C1 exon
chr2:196337997-196338053
Coord A exon
chr2:196338054-196338099
Coord C2 exon
chr2:196338352-196338453
Length
46 bp
Sequences
Splice sites
5' ss Seq
CAGGTAGTA
5' ss Score
5.89
3' ss Seq
TAGAATTTTGGGTTCTCTAGGAC
3' ss Score
6.8
Exon sequences
Seq C1 exon
TTTCTGACATGGCGGAGCCAAGACATGGAGAATTGTGCTGTCCGGGGAAAGCTGACG
Seq A exon
GTGAGGAGTGGAATAGAGTTGGAGGGAAGGCGAGAGCTGCCTTCAG
Seq C2 exon
GACGAATGCTACAACTACATCCGTGTTCTTGTTCCCTGGGACTCGCAGACACTCCTTGCCTGTGGAACAAATTCCTTCAGCCCTGTGTGTCGCAGCTATGGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000021101-9-6,10-6-2/2
Average complexity
Alt5
Mappability confidence:
NA
Protein Impact
ORF disruption when splice site is used (sequence inclusion)
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0140314=Sema=FE(14.3=100)
A:
NA
C2:
PF0140314=Sema=FE(26.2=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Mouse
(mm9)
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:
ATGGAGAATTGTGCTGTCCGG
R:
CATAGCTGCGACACACAGGG
Band lengths:
133-179
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]