RnoINT0133075 @ rn6
Intron Retention
Gene
ENSRNOG00000021101 | Sema6c
Description
semaphorin 6C [Source:RGD Symbol;Acc:3659]
Coordinates
chr2:196340706-196341262:+
Coord C1 exon
chr2:196340706-196340879
Coord A exon
chr2:196340880-196341115
Coord C2 exon
chr2:196341116-196341262
Length
236 bp
Sequences
Splice sites
5' ss Seq
CCGGTAAGT
5' ss Score
10.91
3' ss Seq
TGCTTATGGCATCAAACTAGGTG
3' ss Score
5.84
Exon sequences
Seq C1 exon
GGCTCTACTGACCCAGGTAGCTGTGGATGGTATGGCTGGCCCCCACAGAAATACTACAGTCCTGTTTCTTGGCTCCAATGATGGGACAGTGCTGAAGGTGCTACCTCCAGGGGGACAGTCTCTGGGACCCGAGCCTATCATATTGGAAGAGATTGATGCCTACAGCCATGCCCG
Seq A exon
GTAAGTCCTTTGTGGGGGCAGGTGGGTGATGGGGATGGGGGGATAGGTTGGGTACTCCAGTGTTGGCCTGGCAGGATTAGAGGCTTGAAGTGGAGAAAGGGACTTGGTGAGAAGGCTCCACTGTTGGGTAGGGTGGCTCCATGGGTTGTGCCCTATCACTTCTTTCTTCCCATCAACTGTTTTGGGGACAGGCAGCCTTGCTGTCCCCATTCTGATTGCTTATGGCATCAAACTAG
Seq C2 exon
GTGCAGTGGGAAGCGGTCACCCCGAGCTGCTCGACGGATCATAGGGCTGGAGCTGGACACTGAGGGTCACAGGCTTTTTGTGGCCTTTCCTGGATGCATCGTCTACCTCTCTCTCAGCCGCTGTGCCCGGCATGGAGCATGTCAGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000021101:ENSRNOT00000028645:12
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.051 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0140314=Sema=FE(13.9=100)
A:
NA
C2:
PF0140314=Sema=PD(0.2=2.0),PF0143720=PSI=PU(14.5=18.0)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GCTCTACTGACCCAGGTAGCT
R:
CGGCTGAGAGAGAGGTAGACG
Band lengths:
293-529
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]