DreINT0131122 @ danRer10
Intron Retention
Gene
ENSDARG00000036911 | scamp1
Description
secretory carrier membrane protein 1 [Source:ZFIN;Acc:ZDB-GENE-040426-1803]
Coordinates
chr21:3568118-3568473:-
Coord C1 exon
chr21:3568314-3568473
Coord A exon
chr21:3568220-3568313
Coord C2 exon
chr21:3568118-3568219
Length
94 bp
Sequences
Splice sites
5' ss Seq
CAGGTACAT
5' ss Score
7.79
3' ss Seq
CCTCTCTCTTTCTCTTTCAGGAG
3' ss Score
13.82
Exon sequences
Seq C1 exon
TCCACACGGGGACGCTGTTTGCTAATATCTTCGGCTGTCTGTCGTGGTTCTGTGTGGATGCGTCGAGGGGAGTGGATTTTGGTCTAGCTATGCTCTGGTTTATGCTCTTCACACCCTGCTCTTTTGTCTGCTGGTACAGACCTCTGTATGGAGCGTTCAG
Seq A exon
GTACATGCATGCACGCGCACACACACACACACACACACACACACAGCACCTTTATGCAGAATTCAGTCTAACTGCCTCTCTCTTTCTCTTTCAG
Seq C2 exon
GAGTGACAGCTCTTTTAGGTTCTTTGTATTCTTCTTCGTTTATATCTGCCAGTTTGGTGTCCATGTTCTGCAAGCTATTGGCATTACAGGCTGGGGAGCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000036911:ENSDART00000053596:6
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:
PF041448=SCAMP=FE(29.8=100)
A:
NA
C2:
PF041448=SCAMP=FE(19.1=100)
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:
CGTCGAGGGGAGTGGATTTTG
R:
AGCTTGCAGAACATGGACACC
Band lengths:
176-270
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]