RnoINT0133095 @ rn6
Intron Retention
Gene
ENSRNOG00000004812 | Sema6d
Description
semaphorin 6D [Source:RGD Symbol;Acc:1310910]
Coordinates
chr3:116943294-116944249:+
Coord C1 exon
chr3:116943294-116943454
Coord A exon
chr3:116943455-116944137
Coord C2 exon
chr3:116944138-116944249
Length
683 bp
Sequences
Splice sites
5' ss Seq
ACTGTAAGT
5' ss Score
8.59
3' ss Seq
TAGCCCATTTTCACTTGCAGATT
3' ss Score
8.62
Exon sequences
Seq C1 exon
GAAGCTAAGTGGGACTTCTGAGGAGGGAGCTCAGATACCTTCTCGGCCAACCATGAGGTTCTTTCTGCTGTGGTTCTGTGTGCTGTTCCTTCTGGTCTCCAGGTTACGGGCCGTCAGCTTCCCTGAGGACGATGAGCCCCTTAACACGGTTGACTACCACT
Seq A exon
GTAAGTCACCCAAAGCCATTTCCTGCTTACAAAGGAAGCCTTTCGTTTGTCTTTTTCTGTGTCTATTCATTTTCAGCATCAGAGACAAATTTTAAAATGTCTTTACATTGTTTTGCACATTAAATCATCTGCGTCTTTCCCTCGGCTGTGTGGAAACTGAGCCAGTTCTGTTGGGCGCCATCCTGCAGCAGCCCAGGCGTAGGGATTATACATTTTCAGTAAAAACAGAAAAGACCATTTGCTGACAGTTCTCCATCTTTTACTAATTTATATTCAAGACCTTAAGAGAGGAATTTAGTTAAAACCCTTCCTACAAGTACTATTTCGTTTGTCTTTTTCTGTGTCTATTCATTTTCAGCATCAGAGACAAATTTTAAAATGTCTTTACATTGTTTTGCACATTAAATCATCTGCGTCTTTCCCTCGGCTGTGTGGAAACTGAGCCAGTTCTGTTGGGCGCCATCCTGCAGCAGCCCAGGCGTAGGGATTATACATTTTCAGTAAAAACAGAAAAGACCATTTGCTGACAGTTCTCCATCTTTTACTAATTTATATTCAAGACCTTAAGAGAGGAATTTAGTTAAAACCCTTCCTACAAGTACTATATACAGCTAATCAATGCTGTCTATTGATTCTTCAGCTCCGTAATCCTGACTGATGGGTTAGCCCATTTTCACTTGCAG
Seq C2 exon
ATTCAAGGCAATATCCGGTTTTTAGAGGACGCCCTTCAGGCAACGAATCGCAGCATAGGCTGGACTTTCAGCTGATGTTGAAAATTCGAGACACACTTTATATTGCTGGCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000004812:ENSRNOT00000066101:2
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0140314=Sema=PU(4.0=42.1)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AAGCTAAGTGGGACTTCTGAGGA
R:
GCCAGCAATATAAAGTGTGTCTCG
Band lengths:
270-953
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]