RnoINT0133085 @ rn6
Intron Retention
Gene
ENSRNOG00000021101 | Sema6c
Description
semaphorin 6C [Source:RGD Symbol;Acc:3659]
Coordinates
chr2:196338928-196339242:+
Coord C1 exon
chr2:196338928-196339047
Coord A exon
chr2:196339048-196339153
Coord C2 exon
chr2:196339154-196339242
Length
106 bp
Sequences
Splice sites
5' ss Seq
GAGGTCAGT
5' ss Score
7.7
3' ss Seq
TCCCTGTCTTCCTACCTCAGAGC
3' ss Score
9.67
Exon sequences
Seq C1 exon
AGGGTAGTTTGTACTCAGCCACAGCAGCAGATTTCCAGGCCAGTGATGCTGTGGTTTACAGAAGCCTTGGACCTCAGCCCCCACTCCGTTCTGCAAAGTATGACTCCAAGTGGCTTCGAG
Seq A exon
GTCAGTCATCCTGGGAGCTAGACTGTGCCTGGAGAGGATACACTAGGATGTGTGGGTATGAGTCTCTGAGCAGGTATAGATGCCCTTCCCTGTCTTCCTACCTCAG
Seq C2 exon
AGCCACACTTTGTCTATGCTTTGGAGCATGGAGACCATGTCTACTTCTTCTTCCGAGAAGTCTCTGTGGAGGACGCCCGCCTGGGGAGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000021101:ENSRNOT00000028645:7
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(9.6=100)
A:
NA
C2:
PF0140314=Sema=PD(4.8=20.0),PF0140314=Sema=FE(11.1=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GGGTAGTTTGTACTCAGCCACA
R:
GCGTCCTCCACAGAGACTTCT
Band lengths:
195-301
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]