HsaINT0147515 @ hg38
Intron Retention
Gene
ENSG00000137872 | SEMA6D
Description
semaphorin 6D [Source:HGNC Symbol;Acc:HGNC:16770]
Coordinates
chr15:47759745-47760415:+
Coord C1 exon
chr15:47759745-47759907
Coord A exon
chr15:47759908-47760303
Coord C2 exon
chr15:47760304-47760415
Length
396 bp
Sequences
Splice sites
5' ss Seq
ACTGTAAGT
5' ss Score
8.59
3' ss Seq
TAGCCCATTTTTACTTGCAGATT
3' ss Score
7.48
Exon sequences
Seq C1 exon
GTAGCTCAGTGGCATTTCTGAGCAGGGGCCACCCTGACTTCACCTTGGCCCACCATGAGGGTCTTCCTGCTTTGTGCCTACATACTGCTGCTGATGGTTTCCCAGTTGAGGGCAGTCAGCTTTCCTGAAGATGATGAACCCCTTAATACTGTCGACTATCACT
Seq A exon
GTAAGTCGTCTCAAGAACAGTCTTCTATTCTGAGAAGGAAGCTTTTCTGTTTTTCATTCTGTAAGCATGTTCATTTTCAGAAAGAGGCAGAGATTTTTTATGTCTTAACCTTGAATTTGCATCTGAGTTTATCAGTAATCATTTCCTAGTGTTTGGAGAAAACGGGGCAGTTTTGTTGGGTGCTTTTCTACAGCAACCTGTATATAGGTTATATATTTTGAGTTAAAAAGACCATTTGCTGACATTCACTGCCTTTTATTCATTTATATTCAAGACCTTAAGAGAGGAATTTAGTTAAAACCCTTCTACAACAAGTATATACAGCTAATCAATGCTGTTTATTGATCCCTCAGCTCCATAATCCTGAATGATGGTTTAGCCCATTTTTACTTGCAG
Seq C2 exon
ATTCAAGGCAATATCCGGTTTTTAGAGGACGCCCTTCAGGCAATGAATCGCAGCACAGGCTGGACTTTCAGCTGATGTTGAAAATTCGAGACACACTTTATATTGCTGGCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000137872:ENST00000558014:5
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.002
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0140314=Sema=PU(17.6=42.1)
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:
TCAGTGGCATTTCTGAGCAGG
R:
CTGCCAGCAATATAAAGTGTGTCT
Band lengths:
270-666
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