GgaINT1024753 @ galGal4
Intron Retention
Gene
ENSGALG00000001171 | SEMA6B
Description
sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6B [Source:HGNC Symbol;Acc:HGNC:10739]
Coordinates
chr28:2499502-2500125:-
Coord C1 exon
chr28:2499994-2500125
Coord A exon
chr28:2499652-2499993
Coord C2 exon
chr28:2499502-2499651
Length
342 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGT
5' ss Score
10.67
3' ss Seq
TTGCCATGCCGTGGTGTCAGACC
3' ss Score
3.04
Exon sequences
Seq C1 exon
CATCCCCGGCTCGGCCGTGTGTGCCTTTGACATGACCCAAGTGGCCGCTGTCTTCGAGGGACGCTTCCGGGAGCAGAAATCACCGGAGTCCATCTGGACAGCCGTACCTGAGGACATGGTGCCAAAGCCCAG
Seq A exon
GTGAGTGAGCGACCCATGGGGACAGCGGGGAGGGGGGCAGGGGACAGCCAGGCGGGTGGTGTAAGGAAGGCAGTTGGGGATGGAGGTGGGCAGAGGAGCAGGGATGGGAGTGACCAAGGCTGGTGGTGGGGATCAGAATTGGAGGGGTTGGGAGGGACCTTTGGATGTCCTCCAATCCAACCCTGATGGGGATGGGGATGTCGGGAAGTGGCGTGGGGATAGAGATTGGAATGGTGACACCAGAGCCAATATCAGCAGAGCTGGAGACGGGACTGGGACAGAAGTGGGACAGGGCTCAGCCACGCCGTGGCAGTGCTGAGCTTTGCCATGCCGTGGTGTCAG
Seq C2 exon
ACCCGGGTGCTGTGCGGCCCCGGGGATGCGCTACAACTCCTCCAGCACCTTCCCCGATGAGATCCTCACCTTTGTGAAGACTCACCCACTGATGGATGAAGCGGTGCCATCCCTGGGCAACGCGCCCTGGATTGTCCGCACAATGAGCCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000001171:ENSGALT00000001774:10
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.089 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0140314=Sema=FE(10.4=100)
A:
NA
C2:
PF0140314=Sema=FE(11.8=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:
GGCCGTGTGTGCCTTTGA
R:
CGGCTCATTGTGCGGACAA
Band lengths:
270-612
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]