HsaINT0147490 @ hg19
Intron Retention
Gene
ENSG00000143434 | SEMA6C
Description
sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6C [Source:HGNC Symbol;Acc:10740]
Coordinates
chr1:151108067-151108639:-
Coord C1 exon
chr1:151108487-151108639
Coord A exon
chr1:151108241-151108486
Coord C2 exon
chr1:151108067-151108240
Length
246 bp
Sequences
Splice sites
5' ss Seq
CAGGTATGG
5' ss Score
9.99
3' ss Seq
CCTGAGGCCCTTTCCTCCAGGGC
3' ss Score
6.99
Exon sequences
Seq C1 exon
GCCAGGATCCTGTGCAGGAGTAGGGGGAGCTGCCTTGTTCTCCTCTTCCCGAGACCTCCCTGATGATGTCCTGACCTTCATCAAGGCTCACCCGCTGCTGGACCCCGCTGTACCACCTGTCACCCATCAGCCTCTACTCACTCTCACTAGCAG
Seq A exon
GTATGGGGCTGAAAAACACTGACCACTGCCTCCCTGTTCTCAGCCACCCTCCTCTTTCTTTGACCCAACAAGGTAAACCGCATTGGTGGGAGGAAGAACTTGTGAAAGTAGAAGGGAGAGAGCTAAGAAGGCAACCCTGGGGCCTGGGGGAAGGGCACAGGCACAGCTACCAAGGCAGTTGGGCTCTCCCTGAAATGCTCAGGTTTCCACTAGACAGGTTCCCTGACCTGAGGCCCTTTCCTCCAG
Seq C2 exon
GGCCCTACTGACCCAAGTAGCTGTGGATGGCATGGCTGGTCCCCACAGTAACATCACAGTCATGTTCCTTGGCTCCAATGATGGGACAGTGCTGAAGGTGCTGACCCCAGGTGGGCGATCCGGGGGACCTGAGCCCATCCTCCTGGAAGAGATTGATGCCTACAGCCCTGCCCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000143434-SEMA6C:NM_030913:13
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.066 A=NA C2=0.106
Domain overlap (PFAM):
C1:
PF0140314=Sema=FE(12.1=100)
A:
NA
C2:
PF0140314=Sema=FE(13.7=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:
GCTGCCTTGTTCTCCTCTTCC
R:
GCAGGGCTGTAGGCATCAATC
Band lengths:
296-542
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)