HsaINT0147519 @ hg19
Intron Retention
Gene
ENSG00000137872 | SEMA6D
Description
sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6D [Source:HGNC Symbol;Acc:16770]
Coordinates
chr15:48053527-48053948:+
Coord C1 exon
chr15:48053527-48053628
Coord A exon
chr15:48053629-48053857
Coord C2 exon
chr15:48053858-48053948
Length
229 bp
Sequences
Splice sites
5' ss Seq
AGGGTAAGT
5' ss Score
10.45
3' ss Seq
TATTTACTTTTCTTTTGTAGTTG
3' ss Score
8.44
Exon sequences
Seq C1 exon
GATGAATGCCACAACTTTATCAAAGTATTTGTTCCAAGAAACGATGAGATGGTTTTTGTTTGTGGTACCAATGCATTCAATCCCATGTGTAGATACTACAGG
Seq A exon
GTAAGTATATTTTATGTGATATGCTTCTTTTGATCAACTTTTCTCCCTTCACTGATATGCTGTTAGAGTTGAAATCTTTCTGCTTTCCAGTAATTTGTTTTATCTCTAGTGCAATGAAAGAATAAAGACAGAATTCTTCAAATGGAATTTTAATACAAATAAAATAGTATTGCCTTCAAACGGGCACGTTGAATAGATATGACACTGGCTATTTACTTTTCTTTTGTAG
Seq C2 exon
TTGAGTACCTTAGAATATGATGGGGAAGAAATTAGTGGCCTGGCAAGATGCCCATTTGATGCCAGACAAACCAATGTTGCCCTCTTTGCTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000137872-SEMA6D:NM_153619:6
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=FE(20.4=100)
A:
NA
C2:
PF0140314=Sema=FE(18.5=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:
GATGAATGCCACAACTTTATCAAAG
R:
AGCAAAGAGGGCAACATTGGT
Band lengths:
192-421
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Genotype-Tissue Expression Project (GTEx)
- 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)