RnoINT0132932 @ rn6
Intron Retention
Gene
ENSRNOG00000025167 | Sema4b
Description
semaphorin 4B [Source:RGD Symbol;Acc:1307872]
Coordinates
chr1:142000627-142001124:+
Coord C1 exon
chr1:142000627-142000790
Coord A exon
chr1:142000791-142001061
Coord C2 exon
chr1:142001062-142001124
Length
271 bp
Sequences
Splice sites
5' ss Seq
GAGGTGAGA
5' ss Score
7.66
3' ss Seq
TTTTCCTTCTCCTTCCCCAGCTG
3' ss Score
11.14
Exon sequences
Seq C1 exon
ACTCTGAAGAAAGGCTGATTAGAAAATTTGAAGCTGAAAACATCTCCAACTACACGGCCCTTCTGCTGAGCCAAGATGGCAAGACGCTGTATGTGGGGGCCCGAGAGGCCCTCTTTGCCCTTAACAGCAACCTCAGCTTCTTGCCGGGCGGGGAGTACCAAGAG
Seq A exon
GTGAGAGATGTTTGAGGGTGGCCAGGGGTGGGTGGTTTTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTCTGTCTGTCTGTCTGTCTGTCTGTNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNGCGGGAAGCTGGCCTGCTGGTCAGGATGCTCTGGACGGGACAGGACAGGAGTGTGGCTCTGCATACCCTCTGTGCCCTTGCACACCTATTTTCCTTCTCCTTCCCCAG
Seq C2 exon
CTGCTGTGGAGTGCAGATCCTGACAGGAAGCAGCAGTGCAGCTTCAAGGGCAAGGACCCAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000025167:ENSRNOT00000030914:2
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=0.190
Domain overlap (PFAM):
C1:
PF0140314=Sema=PU(8.4=67.3)
A:
NA
C2:
PF0140314=Sema=FE(4.6=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
ACTCTGAAGAAAGGCTGATTAGAA
R:
GGTCCTTGCCCTTGAAGCTG
Band lengths:
222-493
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]