HsaINT0147499 @ hg19
Intron Retention
Gene
ENSG00000143434 | SEMA6C
Description
sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6C [Source:HGNC Symbol;Acc:10740]
Coordinates
chr1:151111901-151112177:-
Coord C1 exon
chr1:151112114-151112177
Coord A exon
chr1:151111958-151112113
Coord C2 exon
chr1:151111901-151111957
Length
156 bp
Sequences
Splice sites
5' ss Seq
AAGGTGAGG
5' ss Score
9.16
3' ss Seq
TCTTCAACTTATCCCTTCAGTAT
3' ss Score
7.29
Exon sequences
Seq C1 exon
GGATCACGTTTTCTCCTTCGATCTTCAAGCCGAAGAAGAAGGGGAGGGGCTGGTGCCCAACAAG
Seq A exon
GTGAGGGGCTGTGTGGGAAGAGGTGCAGACGTGGAGATGAGGCTGGGAAAGGTCTAATGTGGGTCAGGTGGGTGGGAAGAAGAATCTAAAAGGAGCCATAATGTGAGGAGGGAACCCAGTTGCCCATGATTTTCCCTCTTCAACTTATCCCTTCAG
Seq C2 exon
TATCTAACATGGAGAAGCCAAGATGTGGAGAACTGTGCTGTACGGGGAAAGCTGACG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000143434-SEMA6C:NM_030913:5
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:
PF0140314=Sema=FE(17.5=100)
A:
NA
C2:
PF0140314=Sema=FE(15.0=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Chicken
(galGal4)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GGATCACGTTTTCTCCTTCGA
R:
CTTTCCCCGTACAGCACAGTT
Band lengths:
115-271
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)