RnoINT0133074 @ rn6
Intron Retention
Gene
ENSRNOG00000021101 | Sema6c
Description
semaphorin 6C [Source:RGD Symbol;Acc:3659]
Coordinates
chr2:196340374-196340879:+
Coord C1 exon
chr2:196340374-196340526
Coord A exon
chr2:196340527-196340705
Coord C2 exon
chr2:196340706-196340879
Length
179 bp
Sequences
Splice sites
5' ss Seq
CAGGTACTC
5' ss Score
7.04
3' ss Seq
CCTGAAGCCTACCGCTCTAGGGC
3' ss Score
2.61
Exon sequences
Seq C1 exon
GCCAGGGTCCTGTGCAGGTGTGGGTGCAGCTGCCTTATTCTCCTCCTCTCAAGACCTGCCTGACGATGTCCTGCTCTTCATCAAGGCACACCCACTGCTGGATCCCGCTGTGCCACCTGCCACCCATCAACCTCTCCTCACTCTGACTAGCAG
Seq A exon
GTACTCACTGCCTCCTGCCCTCGGTCACTCCCTTCGTTCTCTGTGTGGCCCACGAGGCGAATCACACTGGGGGAGAGGACCTGTGAAGCAGTAAGAGAATGGGAAGCAAGGCATCTGGGTGCTGCTGGAAGTGCTCAAGCTTTACTAGACATGTCCTCACCTGAAGCCTACCGCTCTAG
Seq C2 exon
GGCTCTACTGACCCAGGTAGCTGTGGATGGTATGGCTGGCCCCCACAGAAATACTACAGTCCTGTTTCTTGGCTCCAATGATGGGACAGTGCTGAAGGTGCTACCTCCAGGGGGACAGTCTCTGGGACCCGAGCCTATCATATTGGAAGAGATTGATGCCTACAGCCATGCCCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000021101:ENSRNOT00000028645:11
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.038 A=NA C2=0.051
Domain overlap (PFAM):
C1:
PF0140314=Sema=FE(12.3=100)
A:
NA
C2:
PF0140314=Sema=FE(13.9=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:
CAAGACCTGCCTGACGATGTC
R:
TATGATAGGCTCGGGTCCCAG
Band lengths:
246-425
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]