RnoINT0133076 @ rn6
Intron Retention
Gene
ENSRNOG00000021101 | Sema6c
Description
semaphorin 6C [Source:RGD Symbol;Acc:3659]
Coordinates
chr2:196341116-196341605:+
Coord C1 exon
chr2:196341116-196341262
Coord A exon
chr2:196341263-196341527
Coord C2 exon
chr2:196341528-196341605
Length
265 bp
Sequences
Splice sites
5' ss Seq
GAGGTGAGA
5' ss Score
7.66
3' ss Seq
CACTACTCAGTCTCCCCTAGGAG
3' ss Score
3.12
Exon sequences
Seq C1 exon
GTGCAGTGGGAAGCGGTCACCCCGAGCTGCTCGACGGATCATAGGGCTGGAGCTGGACACTGAGGGTCACAGGCTTTTTGTGGCCTTTCCTGGATGCATCGTCTACCTCTCTCTCAGCCGCTGTGCCCGGCATGGAGCATGTCAGAG
Seq A exon
GTGAGAGGAGCCTAAGGTCAGATGTGGCTTGGTGACACTTCCTGGGCTAGTAGGAGCTCAGAAAAACTCCCAAGTCTTGGGGATGACAAGGAAATGGAGGAGAGGATGGGGCACCTTTTGTAGTCTGAAGTAGGCAGCCACTAGGGCCTGAAGCAGATTGGGGTGGATGGGATGGAAATGTGGGGGGCGGTAAGCCTCTCCAGCACCAGGGTAAGCAGAGGGCAACAGTAGGGGTAGCAGCTTCACACTACTCAGTCTCCCCTAG
Seq C2 exon
GAGCTGCCTGGCTTCTCTGGACCCATACTGTGGATGGCATCGGTTCCGAGGCTGTGTGAATATCAGGGGACCTGGAGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000021101:ENSRNOT00000028645:13
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=0.025
Domain overlap (PFAM):
C1:
PF0140314=Sema=PD(0.2=2.0),PF0143720=PSI=PU(14.5=18.0)
A:
NA
C2:
PF0143720=PSI=FE(41.9=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:
GTGCAGTGGGAAGCGGTC
R:
AGGTCCCCTGATATTCACACAG
Band lengths:
220-485
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]