RnoINT0132825 @ rn6
Intron Retention
Gene
ENSRNOG00000016512 | Sema3b
Description
semaphorin 3B [Source:RGD Symbol;Acc:1310079]
Coordinates
chr8:116357520-116359001:-
Coord C1 exon
chr8:116358882-116359001
Coord A exon
chr8:116357666-116358881
Coord C2 exon
chr8:116357520-116357665
Length
1216 bp
Sequences
Splice sites
5' ss Seq
ATGGTGAGA
5' ss Score
7.23
3' ss Seq
GTGCCGTCTGTTTTGGCTAGAAC
3' ss Score
5.39
Exon sequences
Seq C1 exon
GGGAAGAGCTGTATTCCGGGGTGGCGGCGGACCTTATGGGCCGGGACTTTACCATCTTTCGAAGCTTGGGTCAGAATCCGAGTCTCCGAACAGAGCCCCATGATTCCCGCTGGCTCAATG
Seq A exon
GTGAGATGCTGGTGGGGCCCCTGGGAGGAGACTGCCCTCCTCCGATAGGGAAGGTGAGATGAGAAAATGAGAAAGCAAGAGAGCACTGTTGAAGTCTCTCCGAGTATCTGTTATTATACCTGAGACAGGCACAGAGGCAGAGGCAGGCAAGAGTCTGAGTCCGTGGGTCTCAGAGAAAGCACACGATGAGATACATTCCTGTGGCCATGANNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNATAAATAGATCTTTAAAAATAAGGGTGAAAGAACAGAAAGGGGAAAAAGGTGTCTGGGTTGAATAAGGAAAGCTATTTTTTTAAGGAGCTGTGAGTTATTAGTAGCTTCCAGAACACAAGAAACCCAGCCAAAGAATTGGATGAGCATCTAGGTAAGGGAAACGATTAGTGCAAAGACCCTGAGACAAGAGCCAGCAATGATAAGGCTCAAACAACCAGTATTGATAGGAAACCCAGACTCTCAAGGTCTGGAGTCCTTTACTATGTGACAGACAGCAGGAGGAACTGAAGCAGGAACAGGGAGTATTTGATCTGCCAGGGAGGAAGATTTGTGAATGAAGGTGAAAACAGATACCCAATCTCCCTCTTCTCCTGGCAAATTAAGGAAAAGTGTGGCATGGTCAGAACTCCTGCAGAGGGGAGAGGGGGCAGCCCACTTGCGCTCGAAGCTGTGGTCTCTACTGCCCCCTCGTGGCAGTTTCTTGCTTTGCAGATGCTGATCGTAATGGGGGGGGTGCGGGGTGTGTGTGCGGGGGTGGGGGTGTGTCCTTGTCGAGGAGGACCAGGAACAAGACCCGCTGATACCGTGCCGTCTGTTTTGGCTAG
Seq C2 exon
AACCCAAGTTTGTCAAGGTCTTTTGGATCCCAGAGAGCGAGAACCCTGATGACGATAAAATCTATTTCTTCTTCCGTGAGTCCGCAGTGGAAGCGGCACCAGCAATGGGGCGCATGACTGTGTCTCGTGTTGGTCAGATCTGCCGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000016512:ENSRNOT00000066296:7
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.098 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0140314=Sema=FE(9.0=100)
A:
NA
C2:
PF0140314=Sema=FE(10.8=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GAAGAGCTGTATTCCGGGGTG
R:
GGCAGATCTGACCAACACGAG
Band lengths:
262-1478
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]