DreINT0156922 @ danRer10
Intron Retention
Gene
ENSDARG00000002127 | stam
Description
signal transducing adaptor molecule (SH3 domain and ITAM motif) 1 [Source:ZFIN;Acc:ZDB-GENE-031118-123]
Coordinates
chr2:31459527-31459770:+
Coord C1 exon
chr2:31459527-31459611
Coord A exon
chr2:31459612-31459694
Coord C2 exon
chr2:31459695-31459770
Length
83 bp
Sequences
Splice sites
5' ss Seq
TGGGTTAGT
5' ss Score
3.1
3' ss Seq
TTATTTGTTGTCTTCTGAAGGCC
3' ss Score
8.79
Exon sequences
Seq C1 exon
AAAAAGCAACAAGTGAGATGAACACAGCTGAGGACTGGGGCCTCATTCTGGACATTTGTGACAAGATCGGACAGTCTCGCACTGG
Seq A exon
GTTAGTAAACAAGCATTTAGCATGTTTTTGAGCGTATCTTTTAAGTTAATGGGTGGTAAAATATTATTTGTTGTCTTCTGAAG
Seq C2 exon
GCCTAAAGAATGCCTGCGATCTATAATGAGGAGAGTGAATCACAAGGATCCCCATGTTGCCATGCAAGCGTTGACG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000002127:ENSDART00000141170:2
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.138 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0079014=VHS=FE(20.6=100),PF136461=HEAT_2=FE(25.7=100)
A:
NA
C2:
PF0079014=VHS=FE(18.4=100),PF136461=HEAT_2=FE(22.9=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:
AAAAGCAACAAGTGAGATGAACACA
R:
GTCAACGCTTGCATGGCAAC
Band lengths:
159-242
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]