HsaINT0145355 @ hg19
Intron Retention
Gene
ENSG00000198794 | SCAMP5
Description
secretory carrier membrane protein 5 [Source:HGNC Symbol;Acc:30386]
Coordinates
chr15:75310211-75310876:+
Coord C1 exon
chr15:75310211-75310312
Coord A exon
chr15:75310313-75310758
Coord C2 exon
chr15:75310759-75310876
Length
446 bp
Sequences
Splice sites
5' ss Seq
CTGGTAAGA
5' ss Score
9.45
3' ss Seq
ACACTGGCCTCTTCCTGCAGCGG
3' ss Score
9.65
Exon sequences
Seq C1 exon
GACTGACAGCTCCTTCAGTTTCATGGCATTCTTCTTTACCTTCATGGCTCAGTTGGTCATCAGCATCATCCAGGCCGTGGGCATCCCAGGCTGGGGCGTCTG
Seq A exon
GTAAGAGGCAGGGGTGTGGCCTGGGGCTGGCAGGGGTGGCGTTGTGGGTGTATCTTTTGCTTACCTTTGTGTGCTAAGCTGTCTAGCCTATGGGGCCTGAGTGATGGGTTGTTGGGAGAGTGAGAGGATTCGGGATAGTGTAGTAGTACAACCATAGCATCAGAGGGAAGGAGAACCTGGCAGTGGTTTCTTGGGGGCTGAGGGGTGTCAGGGATTATAGGAAAACCTGGGGGAAGAAAGTGTTGTATCTGAAGAGCACCTCTGAGCCACAGGGATGGGGTCTTCTTGAGCCACTGGCACAGGTTCTTTGGGTATCAGTAAGATGGTCCCTCTGCATCCAGTGATATGTTTCCTCCCTGTGGCAATGAGACGGTCCCTTCCTCTAGCGGGGGGCTCCTGGGCACCTCTTATCCTGCCCGCAGCCCCACACTGGCCTCTTCCTGCAG
Seq C2 exon
CGGCTGGATTGCTACCATCTCCTTCTTCGGAACGAACATTGGCTCGGCGGTGGTGATGCTAATTCCCACTGTCATGTTCACAGTGATGGCCGTCTTTTCCTTCATCGCCCTCAGCATG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000198794-SCAMP5:NM_138967:5
Average complexity
IR-S
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(34.0=100),PF144761=Chloroplast_duf=PU(23.0=65.7)
A:
NA
C2:
PF041448=SCAMP=FE(39.0=100),PF144761=Chloroplast_duf=FE(39.0=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
ACAGCTCCTTCAGTTTCATGGC
R:
ATGCTGAGGGCGATGAAGGAA
Band lengths:
214-660
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Autistic and control brains
- Pre-implantation embryo development
Other AS DBs:
FasterDB (Includes CLIP-seq data)
AS-ALPS (AS-induced ALteration of Protein Structure, links to PINs)
APPRIS (Selection of principal isoform)
DEU primates (Only for human)