HsaINT0147503 @ hg19
Intron Retention
Gene
ENSG00000143434 | SEMA6C
Description
sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6C [Source:HGNC Symbol;Acc:10740]
Coordinates
chr1:151110187-151110581:-
Coord C1 exon
chr1:151110462-151110581
Coord A exon
chr1:151110276-151110461
Coord C2 exon
chr1:151110187-151110275
Length
186 bp
Sequences
Splice sites
5' ss Seq
GAGGTCAGG
5' ss Score
4.94
3' ss Seq
CCTGTCATTCCCCATCTTAGAGC
3' ss Score
8.16
Exon sequences
Seq C1 exon
AGGGCAGCCTGTACTCAGCCACAGCTGCGGATTTCCAGGCCAGTGATGCTGTAGTTTACAGAAGCCTTGGGCCCCAGCCCCCACTCCGCTCCGCCAAGTATGACTCCAAGTGGCTCCGAG
Seq A exon
GTCAGGGCGGGCCTGGGGAAAGGAGACTGTTATTGGGGAGGAGGCACAGAGGGAGGACTGTGGCGGGGAGCAGGCAAATGGTGTGGTAGTGTGTATGTATGCAATGGGGAGAGCGGTGTGGGGCCAGGAGCTTCTGAGCAGGTACAGATACTCTTCTATACCCTTTCCTGTCATTCCCCATCTTAG
Seq C2 exon
AGCCACACTTTGTCCAGGCCTTGGAGCATGGAGACCATGTCTACTTCTTCTTCCGCGAGGTCTCTGTGGAGGATGCTCGGCTGGGGAGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000143434-SEMA6C:NM_030913:9
Average complexity
IR-C
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(9.5=100)
A:
NA
C2:
PF0140314=Sema=PD(0.1=0.0),PF0140314=Sema=FE(10.9=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:
AGGGCAGCCTGTACTCAGC
R:
AGCCGAGCATCCTCCACAG
Band lengths:
202-388
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)