RnoINT0133084 @ rn6
Intron Retention
Gene
ENSRNOG00000021101 | Sema6c
Description
semaphorin 6C [Source:RGD Symbol;Acc:3659]
Coordinates
chr2:196338637-196339047:+
Coord C1 exon
chr2:196338637-196338727
Coord A exon
chr2:196338728-196338927
Coord C2 exon
chr2:196338928-196339047
Length
200 bp
Sequences
Splice sites
5' ss Seq
CAGGTGTGC
5' ss Score
6.46
3' ss Seq
CCACTCCCTCGTCTCTCCAGAGG
3' ss Score
9.16
Exon sequences
Seq C1 exon
ATAACATCTCTGCAACAGGAGGGTGAGGAGCTGAGTGGGCAAGCTCGATGCCCCTTTGATGCCACCCAGTCCACTGTGGCCATCTCTGCAG
Seq A exon
GTGTGCACCTGGGCATTCGAGAGGCAGGCATGTGAGGGGCTGGAGGGAGTTCCTCTCCCACCCTGGCCTCTCCCCCATGTCCCTGGGTGGAGGGTTGAGATAGGGGCTGGGACCATGCCTAGGTAGATAGACGGGTAGGCCAGTAGGAGACAAGCTGCAGATCCTGAGCTTTCTGTGACCCCACTCCCTCGTCTCTCCAG
Seq C2 exon
AGGGTAGTTTGTACTCAGCCACAGCAGCAGATTTCCAGGCCAGTGATGCTGTGGTTTACAGAAGCCTTGGACCTCAGCCCCCACTCCGTTCTGCAAAGTATGACTCCAAGTGGCTTCGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000021101:ENSRNOT00000028645:6
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.022 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0140314=Sema=FE(23.8=100),PF0140314=Sema=PU(1.5=12.9)
A:
NA
C2:
PF0140314=Sema=FE(9.6=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:
ACATCTCTGCAACAGGAGGGT
R:
CTCGAAGCCACTTGGAGTCAT
Band lengths:
208-408
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]