RnoINT0132891 @ rn6
Intron Retention
Gene
ENSRNOG00000017704 | Sema3f
Description
semaphorin 3F [Source:RGD Symbol;Acc:1308514]
Coordinates
chr8:116450160-116451117:-
Coord C1 exon
chr8:116450998-116451117
Coord A exon
chr8:116450253-116450997
Coord C2 exon
chr8:116450160-116450252
Length
745 bp
Sequences
Splice sites
5' ss Seq
CAGGTAAGC
5' ss Score
9.88
3' ss Seq
TCTATCGCTCATCTTCCCAGGCC
3' ss Score
7.87
Exon sequences
Seq C1 exon
GGAGAGTGTGGGAACTTCGTCAGACTCATCCAGCCCTGGAACCGGACACACCTGTACGTGTGCGGGACCGGTGCCTACAACCCCATGTGCACCTATGTGAACCGTGGCCGTCGCTCACAG
Seq A exon
GTAAGCGCCTGCCAACCCTGGCCCTATGCTGTCCCCTCTGGTGACTGCACACCAAGGTCCTGATGGGAGGATGGGCTTGAGCCCCATCCTTACCACTTTCAAGCCCCGTGGCCTTGGGTGAGTAAGTCATTGAGCTCTCTGAGCCTCAATTCCCTCACCCGGAAGTCGGGTTCACGGTTCCTTTCGAACAGGTCGGTGTGAGGAAGAGGCAGTGAATTTAGTGCTCTCCAGCTAACACTGTGCCTGGCCCATAGTAAGCATTTGCCCTGCATGGGACCACAGTCCTCTTGGCTATGTCTGTGAAGCTGCCAAGTCAGAGGGTCCGGTGGCATCTTTGGTATTCCAGAAGGCTGGGGGCCTGAGCCAGCTTCCACCCTGGGGCCTGGCGGGGAAGAGCTGTCTTCCTCCCCTGGTCCAGGGCTTGGGGGAAGCTGCTTTTTCCCCAGCTCCGCTCCACCCCGCCTGCTTCTGCCCTTTCATTTCCATGTGGGCATGTATGTGAGTTGATGTGACCTCGTAGGGCATGTGTGAGAGTGACCGGACATAAGTGGCACATGGTGTGCAGGCGTGTGCCAATCCTGTGTGTGTGTGTGTGTGTCTGTGTGTACACATGCATATACGGTCTCTGGGGGCCCATGTGTTCATGTGTGTTCCTGGCCTGTGTGGTATGAGAGGCTGGCAGCCCAGGCCCGCTCCCCCAGCCCCTGCCACCCCCAGCTCTAACGTCTATCGCTCATCTTCCCAG
Seq C2 exon
GCCCCACCGTGGACCCAGATGCAGGTGGTCAGAGGCCGAGGCAGCAGGGCCACAGATGGTGCCGACCGCCCGACGCCCACAGCCCCACGCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000017704:ENSRNOT00000024193:5
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=0.742
Domain overlap (PFAM):
C1:
PF0140314=Sema=FE(32.2=100)
A:
NA
C2:
PF0140314=Sema=PD(19.8=77.4)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Human
(hg19)
No conservation detected
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GGAGAGTGTGGGAACTTCGTC
R:
GCGGTCGGCACCATCTGT
Band lengths:
189-934
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]