HsaINT0147455 @ hg19
Intron Retention
Gene
ENSG00000092421 | SEMA6A
Description
sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6A [Source:HGNC Symbol;Acc:10738]
Coordinates
chr5:115813542-115813850:-
Coord C1 exon
chr5:115813710-115813850
Coord A exon
chr5:115813623-115813709
Coord C2 exon
chr5:115813542-115813622
Length
87 bp
Sequences
Splice sites
5' ss Seq
AAAGTATGT
5' ss Score
6.93
3' ss Seq
TGGTCATCCTCTTCCTGCAGAAC
3' ss Score
10
Exon sequences
Seq C1 exon
ATGCAGCTATGATGGAGTCGAAGACAAAAGGATCATGGGCATGCAGCTGGACAGAGCAAGCAGCTCTCTGTATGTTGCGTTCTCTACCTGTGTGATAAAGGTTCCCCTTGGCCGGTGTGAACGATATGGGAAGTGTAAAAA
Seq A exon
GTATGTATTTTGCCTCATTGACAATTAGAAAGTCCATGGTGGCTAGGAAACAGTCCTAGGTAGCTCATGGTCATCCTCTTCCTGCAG
Seq C2 exon
AACCTGTATTGCCTCCAGAGACCCATATTGTGGATGGATAAAGGAAGGTGGTGCCTGCAGCCATTTATCACCCAACAGCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000092421-SEMA6A:NM_020796:14
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=PD(24.6=31.2),PF0143720=PSI=PU(15.3=18.8)
A:
NA
C2:
PF0143720=PSI=FE(40.9=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CATGCAGCTGGACAGAGCAAG
R:
TGGGTGATAAATGGCTGCAGG
Band lengths:
176-263
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)