HsaINT0145336 @ hg19
Intron Retention
Gene
ENSG00000116521 | SCAMP3
Description
secretory carrier membrane protein 3 [Source:HGNC Symbol;Acc:10565]
Coordinates
chr1:155228617-155230241:-
Coord C1 exon
chr1:155230121-155230241
Coord A exon
chr1:155228746-155230120
Coord C2 exon
chr1:155228617-155228745
Length
1375 bp
Sequences
Splice sites
5' ss Seq
CTAGTAAGT
5' ss Score
8.78
3' ss Seq
TGTTTTTTTGTGCCTTACAGCTC
3' ss Score
11.18
Exon sequences
Seq C1 exon
GCCTCAGCTGCAGCAGCCACAGCTGAGCTGCTGAAGAAACAGGAGGAGCTCAACCGGAAGGCAGAGGAGTTGGACCGAAGGGAGCGAGAGCTGCAGCATGCTGCCCTGGGGGGCACAGCTA
Seq A exon
GTAAGTAATAGAGTGGGGAAGAGCATCTGAGAGTTTGGGAGGAGCAAAAACAGGTCTTAAGGGCCTGGGCTCGGCTGGGTGCGGTGGCTCACACCTATAATCCCAGCACTTTGGGAGGCTGAGGTGGGCGGATCACGAGGTCAAGAGATCGAGACCATCCTAGCCAACATGGTGAAACCCTGTATCTACTAAAAATACACACACACAAAAATTAGCTGGGCATGGTGGCGCGCACCTGTAGTCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATCGCTTGAACCCGGGAGGTGGAGGTTGCAGTGAGCCGAGATAGCGCCACTGCACTCCAGCCTGGTGACAGAGTGAGACTCCATCTCAAAAAAAAAAAAAAACACAAACCTGGGCTCTGGAGTCAGACTGCTGAGTTTGAATTTTAGAGATACTGCTTACTAACCATGAGCTTTTAGGGAAGTTACTTAATCTTGAATGCCTCAGTTTCCCTATTTATAAAATGAAAACCACGTTTGCATCCGTTTGACAGGGTTGTTGTGAAGGTTAAACAAAATATATGTGAAGTACTTGGTACAGTGCTTAGATGTTTTAAATAATAATAAACAGTATTAATTTTTCCACTCTCACTTGTCTCCTTGGACCCCAAATTGGAGATAAAAGAGAGGATCCAGGGCTGGGTATGGTGCCTCACGCCTGTAATTCCAACACTTTGGGAGGCCGAGGCAGGCAGGTTGCTTGAGCTCAGGAGTTAGAGACCAACCTGGACAACATAGTGAGATCCTGCCTCCAAAACATTAATGAAAAAAATTAGCAGGGCATGATGGTACCTGTCTGTAGTCCTAGCTCCTCAAGAAGCTGAGGTGGACGGCCAGGCGCCGGGGCTCATGCCTGTAATCCCAGCACTCTGGGAGGCCAAGGCGGGTGGATCACCTGAGGTCAGGAGTTCAGGACCAGCCAACATGGTGAAACCCTGTCTCTACTAAAAATACAAAAATTAGCTGGGCGTGGTGGCATGTGCCCATAATCCCAGCTACTCAGGAGACTGAGGCAGGAGAATTACTTGAACCCGGGAGGCGGAGATTGCACTGAGCCAAGATCACACCACTGCACTCCAACCTGGGCAACAAGAGCGAAACTCTATCTCAGGAGAAAAAAAAAAAAAAAAAAAAGCTGAGGTGGGAGGGTTGCTTGAGCCCAGGAGGTTGAGGCTACAGTGAACCATGATCATACCACTACCTTCCAGCCTGAACAACAGAGACCCTATCTCAAAAAAAAAAAAAAAAAAAAAAGAGAGGATCCAGGGATGGAGAGAAGGGGGAGTGATTCCTTTGTTGGTCTCTGTTTTACTTCTGGGGTCCACCTGTTTTTTTGTGCCTTACAG
Seq C2 exon
CTCGACAGAACAATTGGCCCCCTCTACCTTCTTTTTGTCCAGTTCAGCCCTGCTTTTTCCAGGACATCTCCATGGAGATCCCCCAAGAATTTCAGAAGACTGTATCCACCATGTACTACCTCTGGATGT
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000116521-SCAMP3:NM_052837:3
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.805 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF049918=LicD=FE(36.4=100)
A:
NA
C2:
PF049918=LicD=PD(35.5=88.6),PF041448=SCAMP=PU(23.6=95.5)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AGCTGAGCTGCTGAAGAAACA
R:
ACATCCAGAGGTAGTACATGGTGG
Band lengths:
230-1605
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)