RnoINT0132945 @ rn6
Intron Retention
Gene
ENSRNOG00000016254 | Sema4c
Description
semaphorin 4C [Source:RGD Symbol;Acc:1562837]
Coordinates
chr9:43132538-43132960:-
Coord C1 exon
chr9:43132738-43132960
Coord A exon
chr9:43132651-43132737
Coord C2 exon
chr9:43132538-43132650
Length
87 bp
Sequences
Splice sites
5' ss Seq
CAGGTAGGA
5' ss Score
9.79
3' ss Seq
TATTCCCCTCACCCCTCCAGGAG
3' ss Score
8.73
Exon sequences
Seq C1 exon
TGCATCAACAACTGGCACCGAGACAATGGCTACACCAGTTCTCTGGAGCTGCCCGACAACACCCTTAACTTCATCAAGAAGCACCCGCTGATGGAGGAACAGGTGAAGCCTCGGTTGGGCCGCCCCCTACTTGTAAAGAAGAACACGAACTTCACACATGTGGTGGCCGACAGGATCCTAGGACTTGATGGCGCCACCTATACAGTGTTGTTCATTGGTACAG
Seq A exon
GTAGGAGCGTTAGCTGTGCCCAAGGCTGGGAACCTGGGGAGACCCAGTGACCGATTCCTCATTTACATATTCCCCTCACCCCTCCAG
Seq C2 exon
GAGATGGTTGGCTGCTGAAAGCTGTAAGCCTGGGGCCCTGGATCCACATGGTGGAGGAGCTGCAGGTGTTTGACCAGGAGCCAGTGGAAAGTCTGGTGCTGTCTCAGAGCAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000016254:ENSRNOT00000021956:12
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.013 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0140314=Sema=FE(17.2=100)
A:
NA
C2:
PF0140314=Sema=FE(8.6=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:
GCCGACAGGATCCTAGGACTT
R:
CTTGCTCTGAGACAGCACCAG
Band lengths:
171-258
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]