GgaINT0030292 @ galGal3
Intron Retention
Gene
ENSGALG00000014116 | SCAMP5
Description
NA
Coordinates
chr10:1764482-1764881:-
Coord C1 exon
chr10:1764780-1764881
Coord A exon
chr10:1764600-1764779
Coord C2 exon
chr10:1764482-1764599
Length
180 bp
Sequences
Splice sites
5' ss Seq
CTGGTGAGG
5' ss Score
8.3
3' ss Seq
TGGTTTCTATCTCCCCGCAGCGG
3' ss Score
11.73
Exon sequences
Seq C1 exon
GACAGACAGCTCCTTCAGCTTCATGGCCTTCTTCTTCACCTTCATGGCCCAGCTGGTGATCAGCATCATCCAGGCCGTGGGGATTCCTGGCTGGGGTGTCTG
Seq A exon
GTGAGGACCATGCAGTGGGCACGAAGACGAGCTCAATGGGGAGGTGGTTTTGGGGTGGTGAAGAGCAAAGAGAGCAAGCAGCCCCTCGGTGTCCTAACATCACGGGTAGCTTCTGTCCTTGGGGGAACTGGAAGCAAGAGTCAGGAGGGATGCTGATTGCTGGTTTCTATCTCCCCGCAG
Seq C2 exon
CGGCTGGATTGCAGCAATCTCCTTCTTTGGGACCAATGTGGGGTCAGCTGTGGTGATGCTGATCCCCACCATCCTGTTCACAGGGATGGCAGTCTTCTCCTTCATCGCCCTCACTATG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000014116:ENSGALT00000022849:4
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(19.2=100)
A:
NA
C2:
PF041448=SCAMP=FE(22.0=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CTCCTTCAGCTTCATGGCCTT
R:
ATAGTGAGGGCGATGAAGGAGA
Band lengths:
210-390
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]