DreINT0132533 @ 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
chr8:26568496-26570029:-
Coord C1 exon
chr8:26569974-26570029
Coord A exon
chr8:26568636-26569973
Coord C2 exon
chr8:26568496-26568635
Length
1338 bp
Sequences
Splice sites
5' ss Seq
GAGGTAAAA
5' ss Score
7.3
3' ss Seq
TCTTCATGCGTGTCCCACAGACC
3' ss Score
10.49
Exon sequences
Seq C1 exon
GAGGTTCCGGCGTCAGGATGTGAGGAACGGAGATCCTAATGCCCTCTGCTCAGGAG
Seq A exon
GTAAAACTGCAGTACCGTCAACAGCCTCAAGGAGGAGACATTTCTCTGTTTTTAATATTTATTCACAATGGCAAATAAATGTGGTTCATAAAAGGACAGTTAACCCAAAAATACTGTCATTCAAACCTGTTTGAGTTTCTTTCTTTTGATGAACACAAAAGAAGATATTTTGAAGAATGTTGGAAACTGTTAGCCCCTGACTACAATAGTATTTTGGTTTCCTACGGTTGTCAGTTGCTCACTGAAAAAGTTTCTTTTGTGTTCAACGTAAGAATTAATCTTACAAAAGGTTGGAAGCTCTTATTTTAGGGGTTATTTTTAGGGTTAACTCTCACTTTATTTGATGGTTTACAAATGTGCTCATGAATATCTTAAAATGTTTTTTTCTGTTATAGGACAGTAAGATTAAAACAGAGTAGGGACACATTACTGTTCAAAACTCTGAACTTTTTTGTTTTATGTTGTATTCAGCAAGGATTTATTAATATGATTAAAGCTGAGAGTAAAAATTTTTACTTTGTTACAGATTTCTGATCCGTATAAATTTTTTGTGCTTTGTATTAAGAAATATAAATTCATTAGAAAAAAAGATTGCATCATTGTTTGCAAAAAAGCATTAACCTTAGCTGTTATGGCTGTTGAAAATCTTCATTATCAATAAAACTGAATTAAGGCTGTTTAAATGTTGATCTTTTAGAAAGGATCTTCACTTGTATCATTTAAAAAATAACAACTTTAGTTCATTTCACATTTATAAAAAACTTTTATTTAGGATTTTAATATTTCCTGTTTAGCATTTATCTGCCATTACATTCAAATAGTTATTGTCTTATTTATTAATTTATTTATTTTAAAATGGCTGCATCATCTTTGTTTTGTTTCTTACTATTTATTTTTGTTGTTTTACACCTAAAATATCTACAAAGTCTTAAATCAAAAAGCCATCAGAATTTTAAAAACAAAGTCATTTTTGTTTGCCTAAAATAACACAAATTATCTGTCAGGGTGCTCAAAAAGAGAAATTTAATTGAAACCCTGTAACTTTTTGGACTTTGTAATTTTTCATTGAGCCAGAATCATACATCATACTGATCAGTTTTTTAATAAACAGTTTGGTTTGTCTCTACTTCTCAAGTACACATTGTATATCTTGGTTTAAGTTGTTTGCACTGAAAAACAAAGTCTACATCTGATTTTACTGTCTATGCGGTTCATACAGTATATTTTGTTTACTTTTGTAAAGTGTTATGCACACACTCTTGATATTGAGAGTAAAATTTTAACTACATTTTATTAATGCTTTGAAGTGTAACGTTGTTCTTCATGCGTGTCCCACAG
Seq C2 exon
ACCATCAGAAGCAGCGTGTCCTGGAGAAGAGGTTGTACGCTGTGGATGGAAGCAGCTCCTTCCTGGAATGCGTCCCGAAATCACTGCAGGCCCAGATTACATGGACCTATCAGAAGCTTCCGGAAAACCCACGGGAGGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000011672:ENSDART00000027301:15
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.350 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0143720=PSI=FE(32.2=100)
A:
NA
C2:
PF0143720=PSI=PD(6.8=8.5),PF0248011=Herpes_gE=PU(22.7=53.2)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GTTCCGGCGTCAGGATGTG
R:
CTCCCGTGGGTTTTCCGGAA
Band lengths:
190-1528
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]