HsaINT0147511 @ hg19
Intron Retention
Gene
ENSG00000137872 | SEMA6D
Description
sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6D [Source:HGNC Symbol;Acc:16770]
Coordinates
chr15:48056371-48056990:+
Coord C1 exon
chr15:48056371-48056502
Coord A exon
chr15:48056503-48056834
Coord C2 exon
chr15:48056835-48056990
Length
332 bp
Sequences
Splice sites
5' ss Seq
AAGGTAAAT
5' ss Score
8.88
3' ss Seq
TAACGCTGTTTTCCTTTCAGGCC
3' ss Score
11.19
Exon sequences
Seq C1 exon
CATCCCTGGTTCTGCTGTCTGTGCATTTAGCATGGATGACATTGAAAAAGTATTCAAAGGACGGTTTAAGGAACAGAAAACTCCAGATTCTGTTTGGACAGCAGTTCCCGAAGACAAAGTGCCAAAGCCAAG
Seq A exon
GTAAATAAAAAAGTAGAAAAGGGTTTTGTCTTGAACAAAACCTTCCGGTCATTGGAAGCATCCCTCCTCAGGGAGCAGCTTGGCCAACCTCCCACACCAGGAAGGGGTCCCTCTCTCAGACAGAGCCAGCAGACATAGCCTTGTGACCTGCAAGCCCATGAGTGTGAATGGAGAACCCATTGAATTCAGGGGCATAGCATTGCTCCTTTAGTTTCACTCACTCTCCTTCCTCACTTGACCTCTTCTCTGAGAATATACACTTATTCCTTAGATACAGTACATGGTGTGGCAGGGGCAGCCGAGAGCATAAAATAACGCTGTTTTCCTTTCAG
Seq C2 exon
GCCTGGCTGTTGTGCAAAACACGGCCTTGCCGAAGCTTATAAAACCTCCATCGATTTCCCGGATGAAACTCTGTCATTCATCAAATCTCATCCCCTGATGGACTCTGCCGTTCCACCCATTGCCGATGAGCCCTGGTTCACAAAGACTCGGGTCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000137872-SEMA6D:NM_153619:11
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.111 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0140314=Sema=FE(10.3=100)
A:
NA
C2:
PF0140314=Sema=FE(12.2=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:
ATCCCTGGTTCTGCTGTCTGT
R:
TGACCCGAGTCTTTGTGAACC
Band lengths:
286-618
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)