GgaINT1024709 @ galGal4
Intron Retention
Gene
ENSGALG00000013722 | SEMA3B
Description
sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3B [Source:HGNC Symbol;Acc:HGNC:10724]
Coordinates
chr12:3222988-3223336:+
Coord C1 exon
chr12:3222988-3223107
Coord A exon
chr12:3223108-3223190
Coord C2 exon
chr12:3223191-3223336
Length
83 bp
Sequences
Splice sites
5' ss Seq
ATGGTCAGT
5' ss Score
6.57
3' ss Seq
TGCCACCCATCCACTCCCAGAGC
3' ss Score
7.7
Exon sequences
Seq C1 exon
GCGAGGAGCTCTACTCGGGGGTGGCCACCGATCTGATGGGGCGCGACTTCACCATCTTCCGCAGCATGGGCTCCCGCCCGTCCGTCCGCACGGAGCAGCACGACTCCCGCTGGCTCAATG
Seq A exon
GTCAGTGCCGGGGGGGGTCTCTGCGCCCGGAGGGTCCCTGCGGGCATCCGCAGGCTCTGGATGTGCCACCCATCCACTCCCAG
Seq C2 exon
AGCCCAAGTTCGTGGATGTTTTTTGGGTGCCGGAGAGCGAGAACCCCGACGACGACAAAATCTACTTCTTCTTCCGCGAGACGGCGGTGGAGCGGCAGCAGGGGCTGGGCAAGGCCAGCGTCAGCCGCATCGGCCAGATCTGCAGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000013722:ENSGALT00000035861:6
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(9.2=100)
A:
NA
C2:
PF0140314=Sema=FE(11.0=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:
GAGCTCTACTCGGGGGTGG
R:
ATTTTGTCGTCGTCGGGGTTC
Band lengths:
176-259
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]