HsaINT0145336 @ hg38
Intron Retention
Gene
ENSG00000116521 | SCAMP3
Description
secretory carrier membrane protein 3 [Source:HGNC Symbol;Acc:HGNC:10565]
Coordinates
chr1:155258826-155260450:-
Coord C1 exon
chr1:155260330-155260450
Coord A exon
chr1:155258955-155260329
Coord C2 exon
chr1:155258826-155258954
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:ENST00000302631:4
Average complexity
IR
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:
NO
A:
NA
C2:
PF041448=SCAMP=PU(23.6=95.5)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Rat
(rn6)
No conservation detected
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