DreINT0132531 @ 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
chr8:26570178-26570498:-
Coord C1 exon
chr8:26570457-26570498
Coord A exon
chr8:26570336-26570456
Coord C2 exon
chr8:26570178-26570335
Length
121 bp
Sequences
Splice sites
5' ss Seq
CGGGTAAGA
5' ss Score
9.84
3' ss Seq
GTTCTTCTGTCTCTCTCCAGCAA
3' ss Score
10.95
Exon sequences
Seq C1 exon
GACTCTTCGTCTATTATCAGTATGCAGATTTCCTCCAAACGG
Seq A exon
GTAAGAATACATCTTTTTTGAGAGGAGGGGAAATGTCAGCTATTTTTAAACAAGATCACAGGAGCACATGAAAGCAGCACATCAGTAAATCAAGCGGTGCTGTTCTTCTGTCTCTCTCCAG
Seq C2 exon
CAACAGCTGTATGTTGGCTCAGACACAGGTGTTGTCCAGGTGCCTCTGCACCGCTGCAGTATGTACGGTAAAGCTTGTGCCGAGTGCTGTTTGGCTCGAGATCCGTACTGCGCCTGGGACGGACACACCTGCACACGATACCTGCCAAACACCAAACG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000011672:ENSDART00000027301:13
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(2.9=100)
A:
NA
C2:
PF0143720=PSI=PU(59.3=66.0)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
ACTCTTCGTCTATTATCAGTATGCA
R:
GGTGTTTGGCAGGTATCGTGT
Band lengths:
194-315
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]