RnoINT0132882 @ rn6
Intron Retention
Gene
ENSRNOG00000017704 | Sema3f
Description
semaphorin 3F [Source:RGD Symbol;Acc:1308514]
Coordinates
chr8:116443721-116444582:-
Coord C1 exon
chr8:116444360-116444582
Coord A exon
chr8:116443810-116444359
Coord C2 exon
chr8:116443721-116443809
Length
550 bp
Sequences
Splice sites
5' ss Seq
CAGGTACCC
5' ss Score
8.63
3' ss Seq
TCCTGCCCGGCCCGTTCCAGACC
3' ss Score
6.64
Exon sequences
Seq C1 exon
TGCCCTGGTGGAACCTTTACGCCATCGATGAAGTCCACCAAGGACTATCCTGATGAAGTGATCAACTTCATGCGTACTCATCCACTCATGTACCAGGCCGTCTACCCGCTGCAGCGGCGCCCCCTGGTGGTCCGTACAGGCGCTCCCTACCGCCTCACCACTGTCGCTGTGGACCAGGTGGATGCAGCTGATGGACGCTATGAGGTGCTTTTCCTGGGCACAG
Seq A exon
GTACCCACTGCTGCTCTCAGACCCTCCCCCATTGGGCCCGCCAGATGGGAGGAGCTGATCCTGGGGCCGGATCCTGTCCAGCTAGGGGTTGCTCCCTAGTCAGAATAGCCAAGACTAGGAATGGGAAAACTCCATCTCTCCTCCCATTTTGAGGGGTCTACCCAGGGACCCTTACAAGGACTTAAAAATAACTTGGGATGCAGGGATTTAACTGCTAGCCTGTGTACACACACATGCAAGCGTGCACACGCTTGCTTAAATACATTCGTCGGAATCATAACAGTGTCCAACTCAGTTGCCCATTTCCTGTTCTCAGTAGGGCCCAAAATGAGAGTCTGGGTGCAGGGGCAGACCCTGGCCATGACCCCCTTTGTCCTGTTCTAGTCCCCCCCAAATTCTTCCCTTCATCCAAGGGAGGCCCTTGAACCTCAGCCTGGAAGCCCTGCTCCAATGCCCTAGAGGAGATGGGGCTTTGGTGGGGAAGGGGCTGAGGNTTTGCCCCTTCCCCAGCATCCTCAGCCCCACTGAGGTCCTGCCCGGCCCGTTCCAG
Seq C2 exon
ACCGCGGGACAGTGCAGAAGGTCATCGTGCTGCCCAAGGATGATCAGGAGGTGGAAGAGCTCATGTTAGAGGAGGTGGAGGTCTTCAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000017704:ENSRNOT00000024193:13
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.147 A=NA C2=0.067
Domain overlap (PFAM):
C1:
PF0140314=Sema=FE(15.6=100)
A:
NA
C2:
PF0140314=Sema=FE(6.1=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:
GCCCTGGTGGAACCTTTACG
R:
TTGAAGACCTCCACCTCCTCT
Band lengths:
310-860
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]