HsaINT0147510 @ hg19
Intron Retention
Gene
ENSG00000137872 | SEMA6D
Description
sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6D [Source:HGNC Symbol;Acc:16770]
Coordinates
chr15:48056047-48056502:+
Coord C1 exon
chr15:48056047-48056264
Coord A exon
chr15:48056265-48056370
Coord C2 exon
chr15:48056371-48056502
Length
106 bp
Sequences
Splice sites
5' ss Seq
TAGGTGAGA
5' ss Score
6.95
3' ss Seq
ATGATTTTCTTCCTTTTCAGCAT
3' ss Score
10.51
Exon sequences
Seq C1 exon
GCTGTGTATTCCCGCGTGGCCCGCATATGTAAAAACGACATGGGTGGTTCCCAGCGGGTCCTGGAGAAACACTGGACTTCATTTCTAAAGGCTCGGCTGAACTGTTCTGTCCCTGGAGATTCGTTTTTCTACTTTGATGTTCTGCAGTCTATTACAGACATAATACAAATCAATGGCATCCCCACTGTGGTCGGGGTGTTTACCACGCAGCTCAATAG
Seq A exon
GTGAGAGCAGAACCCCGGCACTGCAAAGATATTCTCTGCATGCCTGTCAGAACCAAGACAGGCTTCATGTCGCCAGCCTCTTCCTGATGATTTTCTTCCTTTTCAG
Seq C2 exon
CATCCCTGGTTCTGCTGTCTGTGCATTTAGCATGGATGACATTGAAAAAGTATTCAAAGGACGGTTTAAGGAACAGAAAACTCCAGATTCTGTTTGGACAGCAGTTCCCGAAGACAAAGTGCCAAAGCCAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000137872-SEMA6D:NM_153619:10
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
In the CDS, with uncertain impact
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.111
Domain overlap (PFAM):
C1:
PF0140314=Sema=FE(16.9=100)
A:
NA
C2:
PF0140314=Sema=FE(10.3=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:
CTCGGCTGAACTGTTCTGTCC
R:
TGGCACTTTGTCTTCGGGAAC
Band lengths:
251-357
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)