GgaINT0029706 @ galGal3
Intron Retention
Gene
ENSGALG00000001689 | SCAMP2
Description
NA
Coordinates
chr10:1817474-1818290:+
Coord C1 exon
chr10:1817474-1817591
Coord A exon
chr10:1817592-1818161
Coord C2 exon
chr10:1818162-1818290
Length
570 bp
Sequences
Splice sites
5' ss Seq
ATCGTGAGT
5' ss Score
8.88
3' ss Seq
CTCTTTTGTCCCTTCCACAGCGA
3' ss Score
10.37
Exon sequences
Seq C1 exon
GCTGTGGCTGCAGCAGCACAGGCCGGGCTGCTTCAGCAGCAGGCAGAACTAGAGAGGAAAGCAGCTGAGCTGGAGAAGAAGGAAAGGGAATTGCAGAACAATGCAGCCAGCATTAATC
Seq A exon
GTGAGTAGTGCTTCCTGCCTTGCCTGCAGCCAAGGTGATGCCTGGGGATGCCCATGGCCACTGGGGAGCTTTGGCCTGTCCAGAGGAATGCCTCTCCTTCTCTAGCTTTTCATGGCTGTGGCAGCCCCCTGGGACTGCATCTGGCCCTCCGTGGCTTGCGGTGTAACTGCCTACTGAAGTGCTGGGCAGGAAATGAGCTCTGAGATGAGCTACTGGAGTCCAGCTCTGGCTTTTTATCGCTCTCGATGCTATCTTAACCAGAGCAAAACAGTATTTTCCCCTAACCTTGAATGATTGAGCCTGGACTCGTAGTCCCAAATGCTCGTGCTCGTCCTTTGGCCATCACATGGAAACTCTGCCTCCCACAGAGGAAAGCTTTCAACTCTAGGCTGCCCTACCTTGCTGCTGCCAGTGGCGTTAATGCACCCCTGCTCAAACCCACTGAGGCCCAGCCTCCCCCAAGGTGTTGATGTCAGTTGATACGAGCACGGCTTGCAAATGAAGGCATGCCAATGGCTCTTCCCACCAGAGAAGAGCAAGCAAAGAACAGCTCTTTTGTCCCTTCCACAG
Seq C2 exon
CGAGACAGAACAACTGGCCACCCCTCCCCAGGAAGTGTCCGATCAAGCCGTGCTTCTATCAGGACTTTTCTGCAGACATCCCAGCTGACTACCAGCGGATATGCAAGATGCTTTACTACTTGTGGATGC
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000001689:ENSGALT00000002583:3
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.475 A=NA C2=0.045
Domain overlap (PFAM):
C1:
PF117403=KfrA_N=FE(40.6=100),PF120723=DUF3552=PU(84.8=97.5)
A:
NA
C2:
PF117403=KfrA_N=PD(3.1=6.8),PF120723=DUF3552=PD(13.0=13.6),PF041448=SCAMP=PU(30.4=95.5)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GCAGCAGGCAGAACTAGAGAG
R:
TCCACAAGTAGTAAAGCATCTTGC
Band lengths:
209-779
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]