HsaINT0147491 @ hg19
Intron Retention
Gene
ENSG00000143434 | SEMA6C
Description
sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6C [Source:HGNC Symbol;Acc:10740]
Coordinates
chr1:151107639-151108240:-
Coord C1 exon
chr1:151108067-151108240
Coord A exon
chr1:151107786-151108066
Coord C2 exon
chr1:151107639-151107785
Length
281 bp
Sequences
Splice sites
5' ss Seq
CCGGTGAGG
5' ss Score
9.35
3' ss Seq
TCCTTCTGGCCTCACCCTAGGTG
3' ss Score
9.83
Exon sequences
Seq C1 exon
GGCCCTACTGACCCAAGTAGCTGTGGATGGCATGGCTGGTCCCCACAGTAACATCACAGTCATGTTCCTTGGCTCCAATGATGGGACAGTGCTGAAGGTGCTGACCCCAGGTGGGCGATCCGGGGGACCTGAGCCCATCCTCCTGGAAGAGATTGATGCCTACAGCCCTGCCCG
Seq A exon
GTGAGGCCTTTGGAGGGCAGGCCCCCTGCAAAGCAGGGAGGGGATGGGAGGTAGCAGCTGCAGATTCGGGAATAGGTTGGAAACATCAACATTGGCTTTTGCAGGGTGGGAGCTCTGGGCTAGACAGGCTTGGCGAGAAGACTGGACAGTGTGGTAGGGCGGGGCAGCTCCATGGGTTGTGCTCAGTTGCTTGTGTGCCTCCCCGCTTTCTGTTCTTCCACTCACTCAGGGAAAAGGTAGCCTCATCTGTCCATCTCTGGTTCCTTCTGGCCTCACCCTAG
Seq C2 exon
GTGCAGTGGGAAGCGGACAGCCCAAACAGCACGACGGATCATAGGGCTGGAGCTGGACACTGAGGGTCACAGGCTTTTTGTGGCTTTTTCTGGCTGTATTGTCTACCTCCCTCTCAGCCGGTGTGCCCGGCATGGGGCCTGTCAGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000143434-SEMA6C:NM_030913:14
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.106 A=NA C2=0.060
Domain overlap (PFAM):
C1:
PF0140314=Sema=FE(13.7=100)
A:
NA
C2:
PF0140314=Sema=PD(1.9=16.0),PF0143720=PSI=PU(14.5=18.0)
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:
GCCCTACTGACCCAAGTAGCT
R:
GGCTGAGAGGGAGGTAGACAA
Band lengths:
292-573
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)