HsaINT0147498 @ hg19
Intron Retention
Gene
ENSG00000143434 | SEMA6C
Description
sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6C [Source:HGNC Symbol;Acc:10740]
Coordinates
chr1:151112114-151112566:-
Coord C1 exon
chr1:151112452-151112566
Coord A exon
chr1:151112178-151112451
Coord C2 exon
chr1:151112114-151112177
Length
274 bp
Sequences
Splice sites
5' ss Seq
CCGGTAAAC
5' ss Score
4.81
3' ss Seq
CTCCTTACCTACCCCCTCAGGGA
3' ss Score
8.42
Exon sequences
Seq C1 exon
GTACTTCCCCATTATCCTGGTTTCGGGGCCTGGAGGATGATGCTGTGGCTGCAGAACTTGGGCTGGACTTTCAGAGATTCCTGACCTTGAACCGGACCTTGCTAGTGGCTGCCCG
Seq A exon
GTAAACTGGCCGTGGCACAGTTGTGGGGCAGACATGCATGCTCCTGGGCAGACTTGGGACCTGTATGGCCACTGTAGCATCTTGCAGGGGACACATGCAGGTGCACAAGCCACGGGGTGTGGACATGCTTGGACCCAGAGCACAAATGCCAAGGCATGGAGGAAGGGGGAAGGGGAGGGCCAGAAGGTCTGCACTGTTTGTCCCTGAACAGCTGACTGTGGGTAAAGTGGGGTGCCTTGACTAGGCTCTGACCCCTCCTTACCTACCCCCTCAG
Seq C2 exon
GGATCACGTTTTCTCCTTCGATCTTCAAGCCGAAGAAGAAGGGGAGGGGCTGGTGCCCAACAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000143434-SEMA6C:NM_030913:4
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=PU(11.7=35.9)
A:
NA
C2:
PF0140314=Sema=FE(17.5=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Chicken
(galGal4)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CTTCCCCATTATCCTGGTTTCGG
R:
CAGCCCCTCCCCTTCTTCTTC
Band lengths:
164-438
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)