RnoINT0132947 @ rn6
Intron Retention
Gene
ENSRNOG00000016254 | Sema4c
Description
semaphorin 4C [Source:RGD Symbol;Acc:1562837]
Coordinates
chr9:43131288-43131602:-
Coord C1 exon
chr9:43131445-43131602
Coord A exon
chr9:43131359-43131444
Coord C2 exon
chr9:43131288-43131358
Length
86 bp
Sequences
Splice sites
5' ss Seq
AGGGTGAGT
5' ss Score
9.25
3' ss Seq
TCACCTCACTTCCCTACCAGGTC
3' ss Score
10.16
Exon sequences
Seq C1 exon
AAGGTGCTGTTTGCTGGCTCCCGTTCTCAACTGGTTCAGCTGTCGCTGGCGGACTGCACGAAGTATCGCTTCTGTGTAGACTGTGTCCTTGCCAGGGACCCCTACTGTGCCTGGAATGTCAACACCAGCCGCTGTGTGGCCACCGGTGGTCATTCAGG
Seq A exon
GTGAGTCAGTAGTCAGTGCCAGGGCCAGGAGGGGAGGCAAATGTGGTTGGAGTCGGACTGCTGATGTCACCTCACTTCCCTACCAG
Seq C2 exon
GTCCCTTCTGGTCCAACACGTGGCAAATTTGGACCCTTCAAAGATGTGTATCCAGTATGCCATTAAAAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000016254:ENSRNOT00000021956:14
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:
PF0143720=PSI=PU(37.6=66.0)
A:
NA
C2:
PF0143720=PSI=FE(25.8=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:
GCTCCCGTTCTCAACTGGTTC
R:
AAGGGTCCAAATTTGCCACGT
Band lengths:
180-266
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]