HsaINT0145328 @ hg19
Intron Retention
Gene
ENSG00000140497 | SCAMP2
Description
secretory carrier membrane protein 2 [Source:HGNC Symbol;Acc:10564]
Coordinates
chr15:75142855-75143822:-
Coord C1 exon
chr15:75143694-75143822
Coord A exon
chr15:75143015-75143693
Coord C2 exon
chr15:75142855-75143014
Length
679 bp
Sequences
Splice sites
5' ss Seq
TGTGTGAGT
5' ss Score
5.84
3' ss Seq
TGTCCTGTCCCCTTCCCCAGTGC
3' ss Score
10.86
Exon sequences
Seq C1 exon
TGAGACAGAACAACTGGCCCCCTCTGCCCTCGTGGTGCCCTGTGAAGCCCTGCTTCTATCAGGATTTCTCCACAGAGATCCCTGCCGACTACCAGCGGATATGCAAGATGCTCTACTATCTGTGGATGT
Seq A exon
GTGAGTCCCACTCCTGCCTTCCAAGCGCAAGGGCGAATTGGGTGTGACTTGAGAGCCCCATCTTGGTCCTGGCTGCTCCTCCCTGGTATACAGGCTTTCAGCAGACTCCAGCCTTCCTCAGTGCCTGGGCTGGGTTGGGGAGATGCCTCTGCCCACAGGCTGCCCCCTGTCTGGAAACCTCCTTGAAAGGGGCAGTCCAGACCACCGATCAGGGAGGGTGGGACTAACTAGAGGCTTCCAAGTTCCTTCAGAGCTCACTGCACTAAAAGGCCCTCCTTAGGTGAAGGCCTTCCCTGCCCACAGGCCTGTGAACTCTGAGGGGTGAGGAAGGAGACTCCCCCTGCAGCTCCATCAGGGGCCATCCAGGGCCAGGGAAAAGCATTGCTAAGAGAAAGACTTCCTTCCCCAAGGACCAGCCCTGGGTCTGCATCCTCCCTCCACACCCCTCAGATACCCGGGCTGTCCCATCACCTCTCAGGAACGTAGTTTGATCCCTGGTTTTGAGGTCCCAGAAAACCAGGATATGGGAACTATCCCTGCCTAGGTACAGAGCGGGCTCCTCTGTTTCAGCAGCTGCCTTCGCAGCATGAACCTCACCTCTCCTAGGGAGTGGCTGCCACATTGGAGCCCCTCAGCCACTGTGGCACAAGTCATAACTCTGTCCTGTCCCCTTCCCCAG
Seq C2 exon
TGCATTCAGTGACTCTGTTTCTGAACCTGCTTGCCTGCCTGGCCTGGTTCTCGGGCAACAGCTCCAAGGGAGTGGACTTTGGCCTCTCCATCCTGTGGTTTCTGATCTTCACTCCCTGTGCCTTCCTTTGTTGGTACCGACCCATCTATAAGGCCTTTAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000140497-SCAMP2:NM_005697:5
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:
PF117403=KfrA_N=PD(7.5=9.1),PF120723=DUF3552=PD(10.6=11.4),PF049918=LicD=PD(34.5=88.6),PF041448=SCAMP=PU(43.8=95.5)
A:
NA
C2:
PF041448=SCAMP=FE(29.6=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:
AGAACAACTGGCCCCCTCTG
R:
AGGCCTTATAGATGGGTCGGT
Band lengths:
279-958
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)