HsaINT0147511 @ hg38
Intron Retention
Gene
ENSG00000137872 | SEMA6D
Description
semaphorin 6D [Source:HGNC Symbol;Acc:HGNC:16770]
Coordinates
chr15:47764174-47764793:+
Coord C1 exon
chr15:47764174-47764305
Coord A exon
chr15:47764306-47764637
Coord C2 exon
chr15:47764638-47764793
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:ENST00000558014:14
Average complexity
IR
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