HsaINT0147304 @ hg19
Intron Retention
Gene
ENSG00000010319 | SEMA3G
Description
sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3G [Source:HGNC Symbol;Acc:30400]
Coordinates
chr3:52473696-52474114:-
Coord C1 exon
chr3:52473883-52474114
Coord A exon
chr3:52473788-52473882
Coord C2 exon
chr3:52473696-52473787
Length
95 bp
Sequences
Splice sites
5' ss Seq
CTGGTAGGA
5' ss Score
6.77
3' ss Seq
CCCCTCCTCCCTGGCCCCAGACT
3' ss Score
8.38
Exon sequences
Seq C1 exon
TGCCCCAGCAAGATGACCGCACAGCCAGGACGGCCTTTTGGCAGCACCAAGGACTACCCAGATGAGGTGCTGCAGTTTGCCCGAGCCCACCCCCTCATGTTCTGGCCTGTGCGGCCTCGACATGGCCGCCCTGTCCTTGTCAAGACCCACCTGGCCCAGCAGCTACACCAGATCGTGGTGGACCGCGTGGAGGCAGAGGATGGGACCTACGATGTCATTTTCCTGGGGACTG
Seq A exon
GTAGGACAGCTGAGCCAGGGTGGCCAGGCTGGAGAGGGGTGTGGGGTCTCTGGCTGTCCCCTCCTGTCCCGCTGACCCCTCCTCCCTGGCCCCAG
Seq C2 exon
ACTCAGGGTCTGTGCTCAAAGTCATCGCTCTCCAGGCAGGGGGCTCAGCTGAACCTGAGGAAGTGGTTCTGGAGGAGCTCCAGGTGTTTAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000010319-SEMA3G:NM_020163:11
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.103 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0140314=Sema=FE(17.3=100)
A:
NA
C2:
PF0140314=Sema=FE(6.7=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TGTCCTTGTCAAGACCCACCT
R:
ACCACTTCCTCAGGTTCAGCT
Band lengths:
168-263
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)