GgaINT1024705 @ 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
chr12:3222219-3222546:+
Coord C1 exon
chr12:3222219-3222376
Coord A exon
chr12:3222377-3222483
Coord C2 exon
chr12:3222484-3222546
Length
107 bp
Sequences
Splice sites
5' ss Seq
AAGGTAACG
5' ss Score
10.19
3' ss Seq
CCCTTCCTTCCCACCCACAGATC
3' ss Score
12.47
Exon sequences
Seq C1 exon
AGCTGCGGGCCCGCCACGGGCTGCGACTCTTCCAGCTGGAGCGCTCGTGCTGCTACGAGGCCCTGCTGCTGGATGAGGAGCGCAGCCGCCTCTTCGTGGGCGCCAAGAACCACCTGCTGTCACTGAGCCTGGACAACATCAGCCAGCGGGACAGGAAG
Seq A exon
GTAACGGGGATGGGTGGAGGTTGGGGGTGTCATCCCGTGGTGCGATGTGTGGGTTTGGTGCCCTTGGCTGGGCGCGGGGATCTGCCACCCTTCCTTCCCACCCACAG
Seq C2 exon
ATCTACTGGCCGGCTCCGGTGGAGTGGAGGGAGGAGTGCAACTGGGCCGGCAAGGACATCACA
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000013722:ENSGALT00000035861:2
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=0.000
Domain overlap (PFAM):
C1:
PF0140314=Sema=PU(7.8=64.2)
A:
NA
C2:
PF0140314=Sema=FE(4.6=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:
GCTGCGACTCTTCCAGCTG
R:
TGTGATGTCCTTGCCGGC
Band lengths:
202-309
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]