RnoINT0132880 @ rn6
Intron Retention
Gene
ENSRNOG00000017704 | Sema3f
Description
semaphorin 3F [Source:RGD Symbol;Acc:1308514]
Coordinates
chr8:116445996-116446354:-
Coord C1 exon
chr8:116446285-116446354
Coord A exon
chr8:116446141-116446284
Coord C2 exon
chr8:116445996-116446140
Length
144 bp
Sequences
Splice sites
5' ss Seq
AGGGTAAGG
5' ss Score
9.16
3' ss Seq
CGTAACCTCTTTACACACAGCTC
3' ss Score
5.52
Exon sequences
Seq C1 exon
AGGACGTGTTTGTCCAGCAGACCCAGGACGTCAGGAACCCAGTCATTTATGCTGTCTTCACCTCTTCAGG
Seq A exon
GTAAGGCTGGAGTTAGGATAAACAGCGGAAGGATTTGGGGGTTATGGTTTATGGACGACCCTGGCCTGGTTCTGAGCTATGAGCTGGGGAGGACTGTGGGTCCAGGCTCTGCCCCAGCCATAGCCGTAACCTCTTTACACACAG
Seq C2 exon
CTCTGTGTTCCGAGGATCTGCAGTGTGTGTCTACTCTATGGCTGACATCCGCATGGTCTTCAATGGGCCTTTTGCTCACAAGGAGGGCCCCAACTACCAGTGGATGCCTTTCTCAGGAAAGATGCCGTATCCCCGGCCTGGCACA
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000017704:ENSRNOT00000024193:11
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=0.041
Domain overlap (PFAM):
C1:
PF0140314=Sema=FE(4.9=100)
A:
NA
C2:
PF0140314=Sema=FE(10.1=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:
GACGTGTTTGTCCAGCAGACC
R:
GTGCCAGGCCGGGGATAC
Band lengths:
212-356
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]