GgaINT0029707 @ galGal4
Intron Retention
Gene
ENSGALG00000001689 | SCAMP2
Description
secretory carrier membrane protein 2 [Source:HGNC Symbol;Acc:HGNC:10564]
Coordinates
chr10:1907371-1908176:+
Coord C1 exon
chr10:1907371-1907499
Coord A exon
chr10:1907500-1908016
Coord C2 exon
chr10:1908017-1908176
Length
517 bp
Sequences
Splice sites
5' ss Seq
TGCGTGAGT
5' ss Score
7.55
3' ss Seq
CTCTCTTCCATCCTGACCAGTGC
3' ss Score
8
Exon sequences
Seq C1 exon
CGAGACAGAACAACTGGCCACCCCTCCCCAGGAAGTGTCCGATCAAGCCGTGCTTCTATCAGGACTTTTCTGCAGACATCCCAGCTGACTACCAGCGGATATGCAAGATGCTTTACTACTTGTGGATGC
Seq A exon
GTGAGTAATGACCTGAACTGCCATAACAATTCTTTCTCTGGAGATTCTGAGTCAAGTGCTGAACTTTGCTCTGCACTAAATGCTGCGGGTGTTGTCTGTACAGGTAAAATAATGCCTTTCTTTCCTGTCTGTGAAGGCATGGCAAGGTCAGCAGGTCGAGTTTTTTTGCTCTGGGAATAGCTCATTTGTCACAGAAGTTTGGTGGTTGTTTAACAGAGGCTTGAGAGTGTGAGGCTCAGAAAGATGGTGGGTAGAGCACTTGGGAGATCAGGTGCAAAACGCTCTCAGCTGCATCTGTCAACGGTGATGCTCTGCAGAGGTTTAAGAGTGGTTTGTAAGCAGCAGGGTTGGATGAGGTGCTTAGGTGGAGCCCTGTTTTCCTTCCAGTGAGGGAAAGGAAATGAGATGGCCTAAAAGGAACTTTTACAGAGCTTTGTGTGTCCAGTGAGAGATGCTTGCAGAGATTTGAGTTGCCTGGGAATTGACTGATGCTTCTTCTCTCTTCCATCCTGACCAG
Seq C2 exon
TGCATTCAGTTACTCTGCTCCTAAACCTGCTCGCTTGCTTGGCATGGTTCATGGTTCACGCAGAAAAAGGAGTAGACTTCGGTCTCTCAATCCTGTGGTTTGTTTTATTCACTCCTTGTGCCTTTCTCTGCTGGTACCGACCGATCTACAAGGCTTTCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000001689:ENSGALT00000002583:5
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.068 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF117403=KfrA_N=PD(3.0=6.8),PF120723=DUF3552=PD(13.0=13.6),PF041448=SCAMP=PU(30.4=95.5)
A:
NA
C2:
PF041448=SCAMP=FE(29.8=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:
AGAACAACTGGCCACCCCTC
R:
AAGCCTTGTAGATCGGTCGGT
Band lengths:
279-796
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]