RnoINT0133081 @ rn6
Intron Retention
Gene
ENSRNOG00000021101 | Sema6c
Description
semaphorin 6C [Source:RGD Symbol;Acc:3659]
Coordinates
chr2:196337797-196338053:+
Coord C1 exon
chr2:196337797-196337860
Coord A exon
chr2:196337861-196337996
Coord C2 exon
chr2:196337997-196338053
Length
136 bp
Sequences
Splice sites
5' ss Seq
AAGGTGAGG
5' ss Score
9.16
3' ss Seq
GACCTCTCTTCTTCCTGCAGTTT
3' ss Score
10.14
Exon sequences
Seq C1 exon
GGATCACGTTTTCTCCTTCGATCTTCAAGCCCAAGAAGAAGGGGAGGGGCTGGTGCCCAACAAG
Seq A exon
GTGAGGGGCTGTATGCGAGGAGGTGCAGGCAGGGAGCCAAAGCTGGGAAAGGCATAACGGGGGTCCTGGGGGCTGAGAAGGAGTCATAATGTGAGGAGGGGTCCAGATTGCCACATGACCTCTCTTCTTCCTGCAG
Seq C2 exon
TTTCTGACATGGCGGAGCCAAGACATGGAGAATTGTGCTGTCCGGGGAAAGCTGACG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000021101:ENSRNOT00000028645:3
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0140314=Sema=FE(16.7=100)
A:
NA
C2:
PF0140314=Sema=FE(14.3=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
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:
GGATCACGTTTTCTCCTTCGA
R:
TTTCCCCGGACAGCACAATTC
Band lengths:
114-250
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]