HsaINT0147520 @ hg38
Intron Retention
Gene
ENSG00000137872 | SEMA6D
Description
semaphorin 6D [Source:HGNC Symbol;Acc:HGNC:16770]
Coordinates
chr15:47761661-47762319:+
Coord C1 exon
chr15:47761661-47761751
Coord A exon
chr15:47761752-47762199
Coord C2 exon
chr15:47762200-47762319
Length
448 bp
Sequences
Splice sites
5' ss Seq
CTGGTAAGA
5' ss Score
9.45
3' ss Seq
AATTATACCTTTGGTTTCAGATG
3' ss Score
7.82
Exon sequences
Seq C1 exon
TTGAGTACCTTAGAATATGATGGGGAAGAAATTAGTGGCCTGGCAAGATGCCCATTTGATGCCAGACAAACCAATGTTGCCCTCTTTGCTG
Seq A exon
GTAAGATCCTTTAGCGTAATGAATATAAATGATTAATGACATTGAAGGTGAAAAAGGAATTTAATGGAAGAGTAAAAGTTAATAACTTGGATACCCACCTTGATCTAAGTGTTCGAAAGGCTAGAATCTATGCACAAATTTCCAAAAAAAGAAGAAATTAAGGGCAAGGATATTTCAGTGCACACTATAAGTATTATGACACCGTGTTGTTAACTAGGCCAGTGGCCCCCGATAAGTTGCTTAAGTTTTTGATGCCTAGATCCCTGTAAAATTAGATAATATCATGGCTGACCTGTCACATGTTGATGGTGAGAATCAGGTGTAGCCCTATTTGTATAGATAATGGTAATACCAGTGAGAGCGCTCCAAAGGGCATAACACGCTGCCAAAGCTAACACACTGCAGGATAATTATGGTTATCTTACCAAAATTATACCTTTGGTTTCAG
Seq C2 exon
ATGGGAAGCTGTATTCTGCCACAGTGGCTGACTTCTTGGCCAGCGATGCCGTTATTTATCGAAGCATGGGTGATGGATCTGCCCTTCGCACAATAAAATATGATTCCAAATGGATAAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000137872:ENST00000558014:10
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(18.5=100)
A:
NA
C2:
PF0140314=Sema=PD(24.1=95.1)
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:
TTGAGTACCTTAGAATATGATGGGGA
R:
GGAATCATATTTTATTGTGCGAAGGG
Band lengths:
198-646
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