DreINT0132529 @ danRer10
Intron Retention
Gene
ENSDARG00000011672 | sema3b
Description
sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3B [Source:ZFIN;Acc:ZDB-GENE-081105-78]
Coordinates
chr8:26572014-26572409:-
Coord C1 exon
chr8:26572190-26572409
Coord A exon
chr8:26572103-26572189
Coord C2 exon
chr8:26572014-26572102
Length
87 bp
Sequences
Splice sites
5' ss Seq
CAGGTACAG
5' ss Score
8.68
3' ss Seq
TCTGTTTTTTTTTCCTGCAGATG
3' ss Score
13.4
Exon sequences
Seq C1 exon
TGTCCCAGTAAGACCTTCGGCAGTTTCGAGTCCACCAAAGGTTTTCCTGATAACGTAATCCAGTTTGCACGGCACCATCCGCTAATGTTTAATCCAGTGACTCCTCTGGGTGGCCGACCGCTGTTCCTGCGCACCGGTATCCCATACACCTTCACTCAGATTACTGTAGACAGAGTCAATGCAGCCGACGGACACTATGATGTCATGTTCATCGGCACAG
Seq A exon
GTACAGTATTGACTGAATATTGAAGAGTGTGTGTTTAGAGGAAGAATACGACTCAGGTTAAAGTCTCTCTGTTTTTTTTTCCTGCAG
Seq C2 exon
ATGTGGGCTCTGTGCTGAAGGTGATCTCGGTGCCCAAGGGAAGCTGGAGCAACACTGAGCTGCTGCTGGAGGAGCTGCACGTCTTTAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000011672:ENSDART00000027301:11
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=FE(16.5=100)
A:
NA
C2:
PF0140314=Sema=FE(6.6=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:
CGGCACCATCCGCTAATGTTT
R:
CACCGAGATCACCTTCAGCAC
Band lengths:
183-270
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]