GgaINT1024756 @ galGal4
Intron Retention
Gene
ENSGALG00000001171 | SEMA6B
Description
sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6B [Source:HGNC Symbol;Acc:HGNC:10739]
Coordinates
chr28:2497656-2498072:-
Coord C1 exon
chr28:2497932-2498072
Coord A exon
chr28:2497734-2497931
Coord C2 exon
chr28:2497656-2497733
Length
198 bp
Sequences
Splice sites
5' ss Seq
GAAGTGAGT
5' ss Score
7.97
3' ss Seq
ACCTCTCTGCTCCCTGCCAGGAG
3' ss Score
9.12
Exon sequences
Seq C1 exon
ATGTGGCCGGGACACAGAGGACGAGCGGAGACTCCTGGGCCTGGAGCTGGACAAGGCAGCCGGGTCCCTGCTGCTGGCCTTCCCCCCCTGTGTGGCCAGGGTGCCCGTGGCTCGCTGCCAGCAGCACTCAGGCTGCATGAA
Seq A exon
GTGAGTGCTGAGAGGGCAGGGCTCGCGGGAGGGATTGTGAAAGGAGAGAGGGCTTCCCATGAATTTGCTCTACACTGGAGTTGAATTATGAATGTTTTAGCATAGCCAGGAGCACCCATGGGGAGAACTGAGGCACGGTGCTGGGTCAGGGTCCCTTTTGGGGGTTGGGGGTTAACTGACCTCTCTGCTCCCTGCCAG
Seq C2 exon
GAGCTGCCTTGGGAGCCGGGACCCGTACTGTGGCTGGACGCCTGAGGGCTCCTGCGTCTTTCTGGAGCCTAGCCCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000001171:ENSGALT00000001774:13
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.083 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0140314=Sema=PD(0.1=0.0),PF0143720=PSI=PU(15.8=18.8)
A:
NA
C2:
PF0143720=PSI=FE(45.6=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:
TGTGGCCGGGACACAGAG
R:
CTAGGCTCCAGAAAGACGCAG
Band lengths:
212-410
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]