DreINT0158036 @ danRer10
Intron Retention
Gene
ENSDARG00000056036 | stxbp1b
Description
syntaxin binding protein 1b [Source:ZFIN;Acc:ZDB-GENE-060531-166]
Coordinates
chr5:28390028-28390477:+
Coord C1 exon
chr5:28390028-28390158
Coord A exon
chr5:28390159-28390369
Coord C2 exon
chr5:28390370-28390477
Length
211 bp
Sequences
Splice sites
5' ss Seq
CATGTAATC
5' ss Score
-2.24
3' ss Seq
TGTGTGTGTGTGTTTATCAGGTA
3' ss Score
10.83
Exon sequences
Seq C1 exon
GGACCCGATAAAGCACGTTCCCAGCTACTGATTTTGGATCGTGGCTTTGACCCTGTTTCGCCACTTCTGCACGAGCTCACGTTTCAGGCCATGGCATATGACCTGCTGCCCATTGAGAATGATGTCTACAT
Seq A exon
GTAATCATTTGTCACTGGCAGTTTGTAATTGAATTATATACTGATCTGAGGTTGCTCAGGAAGCTTGAACTGACCGTCGGCTAAATCCGAGCATTAATCCGTGTCAATATCACCATGCATAATCATATTGTACATGCGCGCTGTAGGCAGATTACTGATGCTGATGGTCCGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTTTATCAG
Seq C2 exon
GTATGAAACCAGTGGTATGGGTGACACTCGTATGAAAGAGGTGCTTCTGGATGAAGATGATGACCTTTGGATGACACTGAGACATAAACACATAGCAGAGGTGTCCAC
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000056036:ENSDART00000005638:9
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=0.054
Domain overlap (PFAM):
C1:
PF0099518=Sec1=FE(7.7=100)
A:
NA
C2:
PF0099518=Sec1=FE(6.5=100),PF140711=YlbD_coat=PU(28.0=75.7)
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:
GACCCGATAAAGCACGTTCCC
R:
GTGGACACCTCTGCTATGTGT
Band lengths:
238-449
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]