HsaINT0147492 @ hg19
Intron Retention
Gene
ENSG00000143434 | SEMA6C
Description
sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6C [Source:HGNC Symbol;Acc:10740]
Coordinates
chr1:151107274-151107785:-
Coord C1 exon
chr1:151107639-151107785
Coord A exon
chr1:151107352-151107638
Coord C2 exon
chr1:151107274-151107351
Length
287 bp
Sequences
Splice sites
5' ss Seq
GAGGTGAGA
5' ss Score
7.66
3' ss Seq
CACACCTCCGTTTTCCCTAGGAG
3' ss Score
10.61
Exon sequences
Seq C1 exon
GTGCAGTGGGAAGCGGACAGCCCAAACAGCACGACGGATCATAGGGCTGGAGCTGGACACTGAGGGTCACAGGCTTTTTGTGGCTTTTTCTGGCTGTATTGTCTACCTCCCTCTCAGCCGGTGTGCCCGGCATGGGGCCTGTCAGAG
Seq A exon
GTGAGAGGGGCCTGAGGCCAGGCCCTGTGTGGGCAAGCTCCCCGGGCCAGCAAGAGCACAGAAACACAGGTCTTTGGGGTGGCAGGAAAACACAGGGGATGGCTGTGGGGTGCCTAGGTACCTCAAGCATTCTGAAGGTGGGCAGCAACCAGGGTGTGGAGAGACTGAGGTGGACAGGAGAGAATGAGGCTGGGAGCCTCCTGTAAGCCAGGGTGGGAAAAGGCAGCAGAATGGAAAGTGACTGGAGTAGAAAGGGATCCAGCCTCACACACCTCCGTTTTCCCTAG
Seq C2 exon
GAGCTGTTTGGCTTCTCAGGACCCATACTGTGGATGGCATAGCTCCAGGGGCTGTGTGGATATCAGGGGATCTGGTGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000143434-SEMA6C:NM_030913:15
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.060 A=NA C2=0.104
Domain overlap (PFAM):
C1:
PF0140314=Sema=PD(1.9=16.0),PF0143720=PSI=PU(14.5=18.0)
A:
NA
C2:
PF0143720=PSI=FE(41.9=100)
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:
GTGCAGTGGGAAGCGGAC
R:
CCACCAGATCCCCTGATATCCA
Band lengths:
225-512
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)