RnoINT0132951 @ rn6
Intron Retention
Gene
ENSRNOG00000016254 | Sema4c
Description
semaphorin 4C [Source:RGD Symbol;Acc:1562837]
Coordinates
chr9:43134676-43135145:-
Coord C1 exon
chr9:43134997-43135145
Coord A exon
chr9:43134739-43134996
Coord C2 exon
chr9:43134676-43134738
Length
258 bp
Sequences
Splice sites
5' ss Seq
GTGGTGAGA
5' ss Score
5.46
3' ss Seq
ATGTCCTGTCCCATCCTCAGATC
3' ss Score
10.33
Exon sequences
Seq C1 exon
AGCTGGTCACAGTAGTGAGGCGGTTCTCCCAGACAGGCATCCAGGACTTCCTGACCCTGACCCTGACAGACCGTTCTGGCCTATTATATGTGGGGGCCCGGGAGGCGCTGTTTGCCTTCAGCGTAGAGGCTCTGGAGCTTCAAGGAGTG
Seq A exon
GTGAGAGGTGGGGCAGTGGGAGGCACTCAGAAGGGAGAGGGAAAGGACTCAGGGTGTGTGTGAACTGTGCGGGCTGGCCCTCAGCCTAGAGGTCTCTCTGGGGGGTGTCAGGTTAGCATTGCTTCCCGCTCCTGGTTTCTGCCAGTTGGGGTGGAATGGGGACCAGGTGCCACCCATTGTGTAGCTTAAGGGGTCCTTTGCAGGCACACACTGAGCACATACCTGTGACATTGCTGATATGTCCTGTCCCATCCTCAG
Seq C2 exon
ATCTCCTGGGAGGCTCCAGCTGAGAAGAAAATTGAGTGTACCCAGAAAGGGAAGAGCAACCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000016254:ENSRNOT00000021956:4
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=0.048
Domain overlap (PFAM):
C1:
PF0140314=Sema=PU(7.7=66.0)
A:
NA
C2:
PF0140314=Sema=FE(4.7=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:
ACAGTAGTGAGGCGGTTCTCC
R:
CTGGTTGCTCTTCCCTTTCTGG
Band lengths:
204-462
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]