RnoINT0132914 @ rn6
Intron Retention
Gene
ENSRNOG00000019737 | Sema4a
Description
semaphorin 4A [Source:RGD Symbol;Acc:1304636]
Coordinates
chr2:187801712-187802089:-
Coord C1 exon
chr2:187801971-187802089
Coord A exon
chr2:187801870-187801970
Coord C2 exon
chr2:187801712-187801869
Length
101 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGA
5' ss Score
9.22
3' ss Seq
TCCCTCCATCTCTTTCCCAGGGT
3' ss Score
9.74
Exon sequences
Seq C1 exon
CTACGGGGTCCCTGCACAAAGCTGTGGTGCCTCAGAATAGCAGTGCTTATCTTGTGGAGGAGATTCAGCTGAGCCCTAACTCTGAGCCTGTTCAGAACCTGCAGCTGGCCCCCACCCAG
Seq A exon
GTGAGAAGGGACCTGAACAGGACAGGGTCTCCCTGTGGGAGGCACCTGGGGAGCCCGGGCCAGGGTGCTAGGGCTCCTGACTCCCTCCATCTCTTTCCCAG
Seq C2 exon
GGTGCAGTGTTCGCAGGCTTCTCTGAAGGCATCTGGAGGGTTCCCAGGGCCAACTGCAGTGTCTATAAGAGCTGTGTGGACTGTGTCCTTGCCAGGGACCCTCACTGTGCCTGGGACCCTGAATCAAGACTGTGCAGCCTTCTGTCTGGCTCTCCCCT
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000019737:ENSRNOT00000056862:12
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.138 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0140314=Sema=FE(9.4=100)
A:
NA
C2:
PF0143720=PSI=PU(62.5=66.0)
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:
CAAAGCTGTGGTGCCTCAGAA
R:
CAGACAGAAGGCTGCACAGTC
Band lengths:
251-352
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]