HsaINT0145354 @ hg19
Intron Retention
Gene
ENSG00000198794 | SCAMP5
Description
secretory carrier membrane protein 5 [Source:HGNC Symbol;Acc:30386]
Coordinates
chr15:75308934-75310312:+
Coord C1 exon
chr15:75308934-75309090
Coord A exon
chr15:75309091-75310210
Coord C2 exon
chr15:75310211-75310312
Length
1120 bp
Sequences
Splice sites
5' ss Seq
CAAGTAAGT
5' ss Score
10.08
3' ss Seq
AGCCACCTCCTCTGCCGCAGGAC
3' ss Score
6.69
Exon sequences
Seq C1 exon
TGAACAGCGTCACGCTGGCCGTGAACCTGGTGGGCTGTCTCGCGTGGCTGATCGGAGGCGGGGGAGCCACCAACTTTGGCCTCGCCTTTCTCTGGCTCATCCTCTTCACACCCTGCTCCTACGTCTGCTGGTTTCGGCCCATTTACAAGGCCTTCAA
Seq A exon
GTAAGTGGTTGGTGCTATCCGCAGTGCCTAGCCGTCTCTGCCCATCTCCCCTGTCTCTTCTCCATATCTTTTCTCACTTCTTTTTTTTTTTTTTTACCCTCCCCCAAACTCACTTTCCCTTGCTCACCTTTGGCTCAGATTGCTAGGTAGGGCCTGGGCTTTCTGGGGGTGCCAAGTTGAGGTGAGAGGGCTGAGAGTTAGTTTCTTTCCTCCTCACTCTACCCTTGGGTGGGGGAAATATAGACAGACCAGGCCTATTTTTTCTTCTGTCATCCCCTTCCTCAGGCAGCTGCATGTTAAATTTTGCCTGTGGGGCTGCCTGTCTTGGTGGAGCTGCCCATCCTAGTACCTGTGGGGCTAGCCGACTTGGTGCCAAGGACACCATCTATCCATGTGCCAATGGGACCAGCCAGCCATGTACCATTGACACTGTTCATGTGCAATGAGGTCATCCAACTGTGTGCCAAAGGGAACACCCATCCACATATCAGTGGGGCTTGCTGTCTTGGTGCCAGTGGGTGTCTACCTAGTGCCAAATGGCATTTTCAATCTTTGTGCCAATGTGACTATTCATCAATGTACCAAGGCTATCTGTCTTGGTGCCAGTAGAATATCCATCTCAATGCTAATGGGGCCTTAAATCTCTTTGTGCCAATCAGGCCATCCATCTAAGTGCCAATTAGCTACTGTTTTGGTGCCAATAGGGTGTCCATTCTAGTTCCAATGAGACTTTCTATCTCTGAGCCTATGAGACCATCCATCCATGTACCAGTGGAGCTAGCTGTCTTGGTGTCATTGTCCATCCCCTTGACAATGAGACTATTTATTCCTGCCTCAGTGGAGCCATCTATTTCTATGCCAATGAGGCCGTCCATCCATGTACCAGTGGGTGGTCTGTTCATGGGAAATCCCTCCCTGTGTAATGTTGCAACACACAGGTCTACCACGTGGAAACTTGCAAAGATGTATGGGTAGAACTAACCCCTTCTGACCTCTCAATTAAGGCCTTTAAATGTCTTCTGTCCATTATGCACTTAAACTTGGAAGGGCTTGGGGGCCTTGAAGGCAGGGAAGCCCTGGCCCTCTGCCCAGGTGACGGGAGCCACCTCCTCTGCCGCAG
Seq C2 exon
GACTGACAGCTCCTTCAGTTTCATGGCATTCTTCTTTACCTTCATGGCTCAGTTGGTCATCAGCATCATCCAGGCCGTGGGCATCCCAGGCTGGGGCGTCTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000198794-SCAMP5:NM_138967:4
Average complexity
IR-C
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=PD(53.3=96.1)
A:
PF041448=SCAMP=FE(54.7=100)
C2:
PF041448=SCAMP=FE(34.0=100),PF144761=Chloroplast_duf=PU(23.0=65.7)
Other Skipping Isoforms:
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CTGGCCGTGAACCTGGTG
R:
CACGGCCTGGATGATGCTGAT
Band lengths:
222-1342
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Genotype-Tissue Expression Project (GTEx)
- 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)