GgaINT0029709 @ galGal4
Intron Retention
Gene
ENSGALG00000001689 | SCAMP2
Description
secretory carrier membrane protein 2 [Source:HGNC Symbol;Acc:HGNC:10564]
Coordinates
chr10:1908672-1910132:+
Coord C1 exon
chr10:1908672-1908773
Coord A exon
chr10:1908774-1910014
Coord C2 exon
chr10:1910015-1910132
Length
1241 bp
Sequences
Splice sites
5' ss Seq
CAGGTAAGC
5' ss Score
9.88
3' ss Seq
TACCCCGCTCTCTCTTCCAGCGG
3' ss Score
10.98
Exon sequences
Seq C1 exon
GTCTGACAGCTCCTTCAGCTTCTTCGTCTTCTTTTTCGTCTTCTTCTGCCAAATAGCAATCTACATCATCCAGGCTGTCGGCATCCCTGGCTGGGGAGACAG
Seq A exon
GTAAGCTCAGCTGAGCAAGCTGGTACAGCCCTGCCCTGGTGTCGGGAGCTATGGGGCCCGGTGCTGCTCTCTTGCTGACAGCTGTCTGTTCCTTCTCCCGTGTCTCTCGCCTGGCACGCAGTGTTGGCAGGTCTCAGCTGGTGCGTCTGTCTGCTCTGCTCATCCTCTCTTAGTCCCAGTGAAGGCACACACGCTTCTGCTGCTGCCACAGCCTTAAAGAAGTGCGTGGAATCTCCCAGTCCTACTCTGCAGTTCTTTTCCTAAGCATTTCCCATCCCGCTGTTACACCGATCGTGTCTCTGAATAGAGCCTTCCCTGGTTGTAGGGAAGGCTTCCTCCCTTCTCCGGGAGCTGTAGCACAGGGCTGAGGAACCTCTCACCCTTTCTTGTTGGCACGGCAGTCCAGGCCCCCACATTGTCCCTCCCCTCACCACAACAACAGCAACGGATTTCTCTTCACCTTGCTGCACATCAGATTCCCACATTCCTGCGGTGCTTTTGAGGAACAGAGAAAAGGTTAACAGCCAGTGCTTTTCCCCCGAGGGAGGGCCTGCAGATGAGTGCAGTGCAACTGCTCTCTATTTTTGCCCGCTGCCTGCAGAGCAGCTCACGGGCAGAGCTGTCCTTGTGCTCCCCCCACCCCTCAGCCATGGGGGACTGGGAGGGGGCGCTCCATTTTTAGTCCAGCGTTGGAGAGCATGCGTTGAACTTTGGGCTCTGTCTCCTCGAGCCAGGCAGCGGATTTATTTTTAGCCTCAGTTGCACGGTGTTGCATTTCTGCTTCTCGTGCACAAGGAGTTGCACAGCACATGGAGTGAGCCAAACCGTCCCGTTGGGTCCCCAGCCTCCTGGTGGCTCGTGGCTGTTCGCTTGCTCAGCTGGAGAGATTCCTTCCTGTGGTGCTGTTCTGAGTGAGGCACGCTGGTGTTCTGCCCCACAGCCAAGCGCTGAGATCTTGTCTTAGGAGCTGGCAGTTGTCACAGGGGAGCTTTTATTTGCAGCCTTTCGCTTCATTCCTTCCTCTTTCTCCCCTTGGAGAGCTGTCACCGTGACACGTAGCTCCGGGCTCCGGATCTGCCATCCAATTCTCAGCCATACCAGCCTCTCTTGACGCAGCCTGGCTACGTTTTGAGGTGTTTGGAGTGACCTGATTTCTGACAGCACCTGCCTGCTGCCTGAAAGCGGGGTGCTGCTGGGGACAGAGCCATAACACACCGTGCTTACCCCGCTCTCTCTTCCAG
Seq C2 exon
CGGCTGGATTGCGGCGCTGTCGGAGCTGCATAGGAACACGGCCGTGGCCATCATCATGATGGTGGTGGCAGGGTTCTTCACGCTCTGTGCAGTCCTCTCGCTCTTCCTCCTCAAGCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000001689:ENSGALT00000002583:7
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(19.1=100)
A:
NA
C2:
PF041448=SCAMP=FE(21.9=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:
GCTCCTTCAGCTTCTTCGTCT
R:
TTGAGGAGGAAGAGCGAGAGG
Band lengths:
208-1449
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]