HsaINT0147519 @ hg38
Intron Retention
Gene
ENSG00000137872 | SEMA6D
Description
semaphorin 6D [Source:HGNC Symbol;Acc:HGNC:16770]
Coordinates
chr15:47761330-47761751:+
Coord C1 exon
chr15:47761330-47761431
Coord A exon
chr15:47761432-47761660
Coord C2 exon
chr15:47761661-47761751
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:ENST00000558014:9
Average complexity
IR
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
Other Skipping Isoforms:
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