RnoINT0133077 @ rn6
Intron Retention
Gene
ENSRNOG00000021101 | Sema6c
Description
semaphorin 6C [Source:RGD Symbol;Acc:3659]
Coordinates
chr2:196341528-196341743:+
Coord C1 exon
chr2:196341528-196341605
Coord A exon
chr2:196341606-196341687
Coord C2 exon
chr2:196341688-196341743
Length
82 bp
Sequences
Splice sites
5' ss Seq
AGGGTAAGT
5' ss Score
10.45
3' ss Seq
CCACCCCCTTTTCCTTCTAGGAC
3' ss Score
12.19
Exon sequences
Seq C1 exon
GAGCTGCCTGGCTTCTCTGGACCCATACTGTGGATGGCATCGGTTCCGAGGCTGTGTGAATATCAGGGGACCTGGAGG
Seq A exon
GTAAGTGAGAAGCCCCTGGGTCTCTGAGGAGAGTGTACAGCAGAGTGCAGAGCCACAGTGAGCCACCCCCTTTTCCTTCTAG
Seq C2 exon
GACTGATGTGGATCTGACTGGGAACCAGGAATCCATGGAGCATGGTGACTGCCAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000021101:ENSRNOT00000028645:14
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.025 A=NA C2=0.917
Domain overlap (PFAM):
C1:
PF0143720=PSI=FE(41.9=100)
A:
NA
C2:
PF0143720=PSI=FE(30.6=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CCTGGCTTCTCTGGACCCATA
R:
CTTGGCAGTCACCATGCTCC
Band lengths:
128-210
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]