RnoINT0132954 @ rn6
Intron Retention
Gene
ENSRNOG00000016254 | Sema4c
Description
semaphorin 4C [Source:RGD Symbol;Acc:1562837]
Coordinates
chr9:43134036-43134364:-
Coord C1 exon
chr9:43134268-43134364
Coord A exon
chr9:43134153-43134267
Coord C2 exon
chr9:43134036-43134152
Length
115 bp
Sequences
Splice sites
5' ss Seq
TGGGTGAGT
5' ss Score
8.73
3' ss Seq
CCTGCTGTTCTCTCCCATAGATG
3' ss Score
12.67
Exon sequences
Seq C1 exon
AACATGCTCACGTTCACCTTGGATCGTGCAGAATTTGAGGACGGGAAGGGTAAATGCCCTTACGACCCAGCTAAGGGCCACACTGGACTCCTTGTGG
Seq A exon
GTGAGTGGTTGCCGCCATCACAGACGGGGGAAACCTGGGATGTCACACTCTGGACTTGCCTTCAGAGCCCATCCTCAGTTTTCTACCTCCTTAGACCTGCTGTTCTCTCCCATAG
Seq C2 exon
ATGGTGAACTGTACTCGGCTACACTCAATAACTTCCTGGGCACAGAGCCGGTTATCCTTCGAAACATGGGGCCCCACCACCCCATCAAGACGGAGTACCTGGCTTTTTGGTTGAATG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000016254:ENSRNOT00000021956:7
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(7.5=100)
A:
NA
C2:
PF0140314=Sema=FE(9.1=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:
ACATGCTCACGTTCACCTTGG
R:
TCAACCAAAAAGCCAGGTACTCC
Band lengths:
210-325
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]