RnoINT0133099 @ rn6
Intron Retention
Gene
ENSRNOG00000004812 | Sema6d
Description
semaphorin 6D [Source:RGD Symbol;Acc:1310910]
Coordinates
chr3:116945483-116946144:+
Coord C1 exon
chr3:116945483-116945573
Coord A exon
chr3:116945574-116946024
Coord C2 exon
chr3:116946025-116946144
Length
451 bp
Sequences
Splice sites
5' ss Seq
CTGGTGAGA
5' ss Score
7.54
3' ss Seq
AATTATAACTTTGGTTTCAGATG
3' ss Score
7.37
Exon sequences
Seq C1 exon
TTGAGTACCTTAGAGTATGATGGGGAAGAAATTAGTGGCCTGGCACGGTGCCCGTTTGATGCCCGACAAACCAATGTTGCCCTCTTTGCTG
Seq A exon
GTGAGAAGCTACAGTGTGTATTGAATATCGCTGATAAATGACATTGACAGTGCAAAGGGAATTTAAAGGAAGACAAAAGCTCACATCTTGGATATATACTTTGACACAAGCATTTCAAAGGGCAAAGCCTAGGAACAAATTATTAAGAAGAATGGGTGAAAAAACAAAAAACAAACAGGTGTATTTCAGTGACTGGTATATGTATTCTTACACGTGGCTCTGTCATTAATTAAGTCTCTGACCCTCAATGCATTGCTTAATTTTTGGTGCTTAGATCCCTCACCTGTAAAATTAGGTAATATCATAGGACAGCCAGTTAGAGGTTGAGGATGAGCGCCAGTGTAGTTTATTGCATAGCTAATGGTGCCAGGTGAAACACTGCAGACGGTAGCCGTGCTAATACTCCATAGGTAATCATGGTTATTTTACCAAATTATAACTTTGGTTTCAG
Seq C2 exon
ATGGGAAACTGTATTCTGCCACAGTGGCTGATTTCCTGGCCAGTGATGCTGTCATTTACAGAAGCATGGGTGATGGATCGGCCCTCCGCACAATAAAATACGACTCCAAATGGATCAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000004812:ENSRNOT00000066101:6
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(7.4=100)
A:
NA
C2:
PF0140314=Sema=FE(9.9=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:
TGAGTACCTTAGAGTATGATGGGGA
R:
TGGAGTCGTATTTTATTGTGCGGA
Band lengths:
198-649
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]