HsaINT0147492 @ hg38
Intron Retention
Gene
ENSG00000143434 | SEMA6C
Description
semaphorin 6C [Source:HGNC Symbol;Acc:HGNC:10740]
Coordinates
chr1:151134798-151135309:-
Coord C1 exon
chr1:151135163-151135309
Coord A exon
chr1:151134876-151135162
Coord C2 exon
chr1:151134798-151134875
Length
287 bp
Sequences
Splice sites
5' ss Seq
GAGGTGAGA
5' ss Score
7.66
3' ss Seq
CACACCTCCGTTTTCCCTAGGAG
3' ss Score
10.61
Exon sequences
Seq C1 exon
GTGCAGTGGGAAGCGGACAGCCCAAACAGCACGACGGATCATAGGGCTGGAGCTGGACACTGAGGGTCACAGGCTTTTTGTGGCTTTTTCTGGCTGTATTGTCTACCTCCCTCTCAGCCGGTGTGCCCGGCATGGGGCCTGTCAGAG
Seq A exon
GTGAGAGGGGCCTGAGGCCAGGCCCTGTGTGGGCAAGCTCCCCGGGCCAGCAAGAGCACAGAAACACAGGTCTTTGGGGTGGCAGGAAAACACAGGGGATGGCTGTGGGGTGCCTAGGTACCTCAAGCATTCTGAAGGTGGGCAGCAACCAGGGTGTGGAGAGACTGAGGTGGACAGGAGAGAATGAGGCTGGGAGCCTCCTGTAAGCCAGGGTGGGAAAAGGCAGCAGAATGGAAAGTGACTGGAGTAGAAAGGGATCCAGCCTCACACACCTCCGTTTTCCCTAG
Seq C2 exon
GAGCTGTTTGGCTTCTCAGGACCCATACTGTGGATGGCATAGCTCCAGGGGCTGTGTGGATATCAGGGGATCTGGTGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000143434:ENST00000368914:15
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.057 A=NA C2=0.081
Domain overlap (PFAM):
C1:
PF0140314=Sema=PD(1.9=16.0),PF0143720=PSI=PU(14.5=18.0)
A:
NA
C2:
PF0143720=PSI=FE(41.9=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:
GTGCAGTGGGAAGCGGAC
R:
CCACCAGATCCCCTGATATCCA
Band lengths:
225-512
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