HsaINT0147298 @ hg19
Intron Retention
Gene
ENSG00000001617 | SEMA3F
Description
sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3F [Source:HGNC Symbol;Acc:10728]
Coordinates
chr3:50212529-50214294:+
Coord C1 exon
chr3:50212529-50212621
Coord A exon
chr3:50212622-50214200
Coord C2 exon
chr3:50214201-50214294
Length
1579 bp
Sequences
Splice sites
5' ss Seq
CAGGTGGGC
5' ss Score
8.07
3' ss Seq
AGCCCCGCTCTGCCTTACAGGAT
3' ss Score
9.08
Exon sequences
Seq C1 exon
GCCACACCATGGACCCAGACTCAGGCGGTCAGAGGCCGCGGCAGCAGAGCCACGGATGGTGCCCTCCGCCCGATGCCCACAGCCCCACGCCAG
Seq A exon
GTGGGCCTCATCCCTCCAGGCCTTTGCCAGGCAGCACTGCCTCTGAGCGGAACTCACCCTGGGCCTGCACCTGAGGCCAGCCTCCCCAGGGCCTCCCCTCTACCTCTGTGCCCACACCCTGTCCCCACCCCTTCCCCTGAAGAGCCCTCAGGCTCAGAAGGCATGCCCAGCTGGACTCATGTCAGCCTCAGTGTGACCCCTGCAGGCAAGAAATAATGAAGCCGCCAGGTGGGGAAGACAGGAGCCCTGGGGACAGCCATGCCTTAGCCCTCAGAAAGCATGTGTGTAGACACACAAGAGCACACACCGGTGTGGATGTGGGCCTTCCTCACTCAGCACCCAGAGTGGAAAGTGGCACATGAGTGCAGTCTGACACCTTACTCCCAGGTGTTCGTGCCCCATGCCTCCCATGAGTCATCTGTGGACACAGGTGTCCTGCACACTCATGTGCTTGGGGCGCTCTTCTCCCGTGTGGTATCTGTCCACTAGTGATGACCTGGGTCTGGGCTGGGAGAGCTGGGGCTGGGCAGGGGCGGGCAGGGGGGCAGGGGCTGCCGGTGAATGACAGAGCATGTTTGTGGTGGGGAGTGCAGAAATGCAGGATCGTGTGGATTCTGTGTGTGTGTGTCCATGGTGTGAGCAGGCGGTTCCGTGTGCTGGCGGTGATATGTTCAGAGCTGTGTGTGCACCCTTGTGTGTGCAGGAAGTCACGTGTGCAGTGTGTAGCTGGAAGTAGGCCTGTGTGCACCTTCCCATCGCCATCCTGCCACCTGCTGCCACCTCCTCCTGCCTCTGTTCCTCTCTCCTTGCCCCTTTCCTTCCCTCTGCCTGGCTTTCTCTTGTGGCCTCTGTGCTCACCCCTGTCCCAGTGCCTTTTCCAGCCTTCCTAGCATCTTGCAGGCTGGGCTGGGAGGCACAGGGGGCTTTGTGAATTCCATGTGGTCTGGGCTGGACTCCTTGACTCCTGGCTCCCTGGGGAGATGTGGAGCCTGGGGGCTGTGCTGAGGGACAGGAGAAAGGTCATGGCCCATTGGTCCATCCTGAGGACCACAGGTAGGACACAAAGCCTGAGGATACAGTAACCTTAGAGCTCTCTGGCCTGGCTAGACCTGATGGCAAAGGACAGGACCCCAGGCCCTTAACCAGTCACTCCTGCCCTGGCCAGGTCTGCAGCGCTTTCTTGACCCAAGACAGGCAGCCACAGCAAAGAGCTGTGCCTCTGTAGCCCAGGGGGCCTTGGCCAGTGTCTTTATGAGCCAGTTGGCATGGAGGGGCTTCAGCCCCTACAAGCCCACTCCATGTCCATCTCATAGCCCACAAGGCAGGGCCCCTTGAGACTTGGTCCCCAGGTCTTCCCTAAGACCTGGGACTAGGAAGCACCCCCCTTGGAGCCCACAGCATGGCCCTGCCCTGGGAGACCTGGCTGGATGGAGTTTAAGGCCAAGGAATGCTGGGGAGTGTAGGGGGTGGGCTCGGGGTATGCCTGGGGGCTCATTCTCACCCTGGGAGCCTGGTGACCCTTACACTTCCTGGCTGGGGGACTGGCCTGGACGATGCTGAGCCCCGCTCTGCCTTACAG
Seq C2 exon
GATTACATCTTCTACCTGGAGCCTGAGCGACTCGAGTCAGGGAAGGGCAAGTGTCCGTACGATCCCAAGCTGGACACAGCATCGGCCCTCATCA
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000001617-SEMA3F:NM_004186:6
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.710 A=NA C2=0.027
Domain overlap (PFAM):
C1:
PF0140314=Sema=FE(18.2=100)
A:
NA
C2:
PF0140314=Sema=PD(22.6=93.8)
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:
ACACCATGGACCCAGACTCAG
R:
GATGAGGGCCGATGCTGTG
Band lengths:
183-1762
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
Other AS DBs:
FasterDB (Includes CLIP-seq data)
AS-ALPS (AS-induced ALteration of Protein Structure, links to PINs)
APPRIS (Selection of principal isoform)
DEU primates (Only for human)