RnoINT0133097 @ rn6
Intron Retention
Gene
ENSRNOG00000004812 | Sema6d
Description
semaphorin 6D [Source:RGD Symbol;Acc:1310910]
Coordinates
chr3:116944795-116945248:+
Coord C1 exon
chr3:116944795-116944855
Coord A exon
chr3:116944856-116945146
Coord C2 exon
chr3:116945147-116945248
Length
291 bp
Sequences
Splice sites
5' ss Seq
AAGGTGAGC
5' ss Score
9.6
3' ss Seq
TGTAATTATTTTTACTTTAGGAT
3' ss Score
8.96
Exon sequences
Seq C1 exon
GGATCAAGTCTATACAGTGAACTTAAATGACATCCCCCAAACAGAGGTGATCCCGAGCAAG
Seq A exon
GTGAGCAGCTAGACACAGAGGGCGAGTGCGCCCTCCCACACTCCCCTGAGCTTCAGTCATGCCCGCCCCCCACTCAGAGTGCATCCGGTTAACACTGAGCTTTGATTTTACTTGATTAATCTAGAAGCTGACATGGAGGTCCAGACAGCAGGATCGAGAAAATTGTGCTATGAAAGGCAAGCATAAAGTGAGTGCAGTGGACGGGTGCCTGCGCAGTCCCTCTTGGTGGCCTCGCCACCATGACATCACCATAGGAGATGTCTGACCGACCTGTAATTATTTTTACTTTAG
Seq C2 exon
GATGAATGTCACAACTTCATCAAAGTCTTTGTCCCAAGAAATGATGAGATGGTTTTTGTCTGTGGCACCAACGCTTTCAACCCGATGTGCAGATACTATAGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000004812:ENSRNOT00000066101:4
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(5.0=100)
A:
NA
C2:
PF0140314=Sema=FE(8.2=100)
Main Inclusion Isoform:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Human
(hg38)
No conservation detected
Mouse
(mm10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CAGTGAACTTAAATGACATCCCCCA
R:
CCTATAGTATCTGCACATCGGGT
Band lengths:
149-440
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]