DreINT0158005 @ danRer10
Intron Retention
Gene
ENSDARG00000001994 | stxbp1a
Description
syntaxin binding protein 1a [Source:ZFIN;Acc:ZDB-GENE-050626-106]
Coordinates
chr21:13809380-13809719:+
Coord C1 exon
chr21:13809380-13809518
Coord A exon
chr21:13809519-13809609
Coord C2 exon
chr21:13809610-13809719
Length
91 bp
Sequences
Splice sites
5' ss Seq
ACGGTTAGA
5' ss Score
4.22
3' ss Seq
TCTTCTGTGTGGTGAAACAGGGA
3' ss Score
6.29
Exon sequences
Seq C1 exon
GATCTCGCAATGGGAACAGATGCTGAGGGTGAGAAGATTAAAGACCCCATGAGGGCCATCGTGCCAATCTTGCTGGATGCCAATGTCACCACCTATGACAAGATCCGCATCATCCTGCTCTACATTTTCCTCAAGAACG
Seq A exon
GTTAGAAGATAGAGAGTTTCGGGCGGTGATTTTAAACCTCTGTTTGTGTTTTACAGCCATTTTGTAACATGTCTTCTGTGTGGTGAAACAG
Seq C2 exon
GGATCACGGAGGAAAACCTTAACAAGCTGATCCAGCATGCTCAGATCCCTCCTGAGGACAGTGAGATCATCACCAATATGGCTCACCTGGGCGTCCCCATCATCACAGAC
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000001994:ENSDART00000015629:14
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.085 A=NA C2=0.135
Domain overlap (PFAM):
C1:
PF0099518=Sec1=FE(8.3=100),PF140711=YlbD_coat=PD(0.9=2.1)
A:
NA
C2:
PF0099518=Sec1=FE(6.5=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:
TCGTGCCAATCTTGCTGGATG
R:
CCCAGGTGAGCCATATTGGTG
Band lengths:
172-263
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]