HsaINT0145327 @ hg38
Intron Retention
Gene
ENSG00000140497 | SCAMP2
Description
secretory carrier membrane protein 2 [Source:HGNC Symbol;Acc:HGNC:10564]
Coordinates
chr15:74851353-74852186:-
Coord C1 exon
chr15:74852069-74852186
Coord A exon
chr15:74851482-74852068
Coord C2 exon
chr15:74851353-74851481
Length
587 bp
Sequences
Splice sites
5' ss Seq
ATGGTAAGG
5' ss Score
9.33
3' ss Seq
ACTCTTTTTGCCCTACCCAGTGA
3' ss Score
6.51
Exon sequences
Seq C1 exon
GCCGTGGTGTCTGCAGCCCAGGCAGGCCTGCTCCGGCAGCAGGAAGAACTGGACAGGAAAGCTGCCGAGCTGGAACGCAAGGAGCGGGAGCTGCAGAACACTGTAGCCAACTTGCATG
Seq A exon
GTAAGGGAGGCTGCTGGGGCCTGGGGCTGCCCTGCCTGGCATAGAAGAGTGTCCTGAAACCTGTGCGGAGGGCCTCCCAGCATTCACCCTGAGCTGCCTTAGAGTTTTGTGGGGCTCTTCTCATCACAGGATGCTGGTCCTGGGAAGAGCAGTAAGTTGCAAGTCAGGAGACCTGCAGTGTAGTTGTAATGGCTGTAGATTACTTCTGCACTCCTTCCTAGCTCTCAAATTCCTTGATTCTTTGATAGCATAGGGGCTTTGGTCCCACAATTCCTTGCTAATGATGATGAACTGAGTTCTCACACTTATGGGCTGCTTGTTAATAAAAATAATCACTTAGGCCATTTAGCTGTCTGTATTTCCCAGTGCATTTGGGGTCTTTTATCTCCATGTGAGCTTGTTGGTATCTCTTTGGGTTCCATTATCCTGTTCTGTCCCACTCCATGCTCCATGCAGACTCCAAGCCCCGCTTGCTGGAGCCCCTCTGGGAACCCTGGTTTGGCCCATACACTATGCTGGCGTGCATGCACCTTGATGCCCCTTCTGAGGCTGGGCCCTTACCTCGTCACTCTTTTTGCCCTACCCAG
Seq C2 exon
TGAGACAGAACAACTGGCCCCCTCTGCCCTCGTGGTGCCCTGTGAAGCCCTGCTTCTATCAGGATTTCTCCACAGAGATCCCTGCCGACTACCAGCGGATATGCAAGATGCTCTACTATCTGTGGATGT
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000140497:ENST00000268099:4
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.229 A=NA C2=0.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF041448=SCAMP=PU(23.5=95.5)
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:
GTGGTGTCTGCAGCCCAG
R:
TCCACAGATAGTAGAGCATCTTGC
Band lengths:
241-828
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