DreINT0156923 @ 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
chr2:31459695-31459988:+
Coord C1 exon
chr2:31459695-31459770
Coord A exon
chr2:31459771-31459892
Coord C2 exon
chr2:31459893-31459988
Length
122 bp
Sequences
Splice sites
5' ss Seq
ACGGTAAGG
5' ss Score
10.38
3' ss Seq
AAGTGTTTTCTGTTCCACAGCTA
3' ss Score
7.63
Exon sequences
Seq C1 exon
GCCTAAAGAATGCCTGCGATCTATAATGAGGAGAGTGAATCACAAGGATCCCCATGTTGCCATGCAAGCGTTGACG
Seq A exon
GTAAGGCAAGCGACTGCTAATGCTAGTAAATGAGGAGGAAGCATGCTTTTATCTCAAGTATGCAAACATCAGAAGCCATTAATGAGCGGTTGAGACTGAAACAAGTGTTTTCTGTTCCACAG
Seq C2 exon
CTACTCGGTGCATGTGTGTCAAACTGTGGAAAGATATTCCATTTAGAGGTCTGCTCCAGGGAATTTGCTAGTGAAGTTAGCAATGTGCTAAATAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000002127:ENSDART00000141170:3
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:
PF0079014=VHS=FE(18.4=100),PF136461=HEAT_2=FE(22.9=100)
A:
NA
C2:
PF0079014=VHS=FE(22.8=100),PF136461=HEAT_2=FE(28.4=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:
GCCTAAAGAATGCCTGCGATCT
R:
GCACATTGCTAACTTCACTAGC
Band lengths:
164-286
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]