HsaINT0147300 @ hg38
Intron Retention
Gene
ENSG00000001617 | SEMA3F
Description
semaphorin 3F [Source:HGNC Symbol;Acc:HGNC:10728]
Coordinates
chr3:50182284-50182783:+
Coord C1 exon
chr3:50182284-50182403
Coord A exon
chr3:50182404-50182643
Coord C2 exon
chr3:50182644-50182783
Length
240 bp
Sequences
Splice sites
5' ss Seq
ACGGTAAGC
5' ss Score
9.89
3' ss Seq
CTGACCCCTGCCACCTGCAGACC
3' ss Score
9.5
Exon sequences
Seq C1 exon
ATGAGGAGCTCTATGCTGGTGTGTACATCGATTTTATGGGCACTGATGCAGCCATCTTCCGCACACTTGGAAAGCAGACAGCCATGCGCACGGATCAGTACAACTCCCGGTGGCTGAACG
Seq A exon
GTAAGCGCAGCCCCAGGAGCCCTTCCGTGGCCATGTGTCTGGGATGCGGCAAGGAGGTCGTAAAGAAGCACATGTGGGGGAAGTGGGGACATGTTTAGCCTATGACTACCTGGGGCAGGGGTAGTTTCTTATCTGGAGAGGAGTTGGGGGTGTTCTTGCACCTGGCTGGGGATTCTGTTGGAGAACATCAGGGGCACCATCAGAGTAGGGGCTCACCCAGCTGACCCCTGCCACCTGCAG
Seq C2 exon
ACCCGTCGTTCATCCATGCTGAGCTCATTCCTGACAGTGCGGAGCGCAATGATGATAAGCTTTACTTCTTCTTCCGTGAGCGGTCGGCAGAGGCGCCGCAGAGCCCCGCGGTGTACGCCCGCATCGGGCGCATTTGCCTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000001617:ENST00000002829:8
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=0.008
Domain overlap (PFAM):
C1:
PF0140314=Sema=FE(19.2=100)
A:
NA
C2:
PF0140314=Sema=PD(19.2=95.2)
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:
GCTCTATGCTGGTGTGTACATCG
R:
GTACACCGCGGGGCTCTG
Band lengths:
229-469
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