RnoINT0132944 @ rn6
Intron Retention
Gene
ENSRNOG00000016254 | Sema4c
Description
semaphorin 4C [Source:RGD Symbol;Acc:1562837]
Coordinates
chr9:43132738-43133207:-
Coord C1 exon
chr9:43133063-43133207
Coord A exon
chr9:43132961-43133062
Coord C2 exon
chr9:43132738-43132960
Length
102 bp
Sequences
Splice sites
5' ss Seq
TCGGTGAGT
5' ss Score
11.11
3' ss Seq
CACACCCTTCCCCGACACAGTGC
3' ss Score
5.31
Exon sequences
Seq C1 exon
GGGTGATATGGACCTGTCAGCAGTCTGCGAGTACCAGTTGGAACATATCCAGCAGGTGTTTGAGGGTCCCTTCAAGGAGTACAGCGAGCAAGCCCAGAAGTGGGCCCGCTATACTGACCCAGTACCCACCCCCCGGCCCGGTTCG
Seq A exon
GTGAGTTTTCGGCATGGGGATGTGCTCCTGACATCAACTCCAGGACCCGCTCATTCACCAGCTGACTGACGGCCGTCCTCCCCACACCCTTCCCCGACACAG
Seq C2 exon
TGCATCAACAACTGGCACCGAGACAATGGCTACACCAGTTCTCTGGAGCTGCCCGACAACACCCTTAACTTCATCAAGAAGCACCCGCTGATGGAGGAACAGGTGAAGCCTCGGTTGGGCCGCCCCCTACTTGTAAAGAAGAACACGAACTTCACACATGTGGTGGCCGACAGGATCCTAGGACTTGATGGCGCCACCTATACAGTGTTGTTCATTGGTACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000016254:ENSRNOT00000021956:11
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.041 A=NA C2=0.013
Domain overlap (PFAM):
C1:
PF0140314=Sema=FE(11.2=100)
A:
NA
C2:
PF0140314=Sema=FE(17.2=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GAAGTGGGCCCGCTATACTGA
R:
CACTGTATAGGTGGCGCCATC
Band lengths:
256-358
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]