HsaINT0147288 @ hg19
Intron Retention
Gene
ENSG00000001617 | SEMA3F
Description
sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3F [Source:HGNC Symbol;Acc:10728]
Coordinates
chr3:50222025-50222964:+
Coord C1 exon
chr3:50222025-50222247
Coord A exon
chr3:50222248-50222875
Coord C2 exon
chr3:50222876-50222964
Length
628 bp
Sequences
Splice sites
5' ss Seq
CAGGTACCC
5' ss Score
8.63
3' ss Seq
CCCTGCCCGGCCCGTTCCAGACC
3' ss Score
7.03
Exon sequences
Seq C1 exon
TGCCCTGGTGGAACCTTCACGCCATCTATGAAGTCCACCAAGGATTATCCTGATGAGGTGATCAACTTCATGCGCAGCCACCCACTCATGTACCAGGCCGTGTACCCTCTGCAGCGGCGGCCCCTGGTAGTCCGCACAGGTGCTCCCTACCGCCTTACCACTATTGCCGTGGACCAGGTGGATGCAGCCGACGGGCGCTATGAGGTGCTTTTCCTGGGCACAG
Seq A exon
GTACCCACTGCTGCTCCCGGCCTCTCCCACGCTGGGCCCACCGGGTGCGGGGTGCAGATCCTTGGGGCTGGGGCTTGCCCTGCTAGGGCTTGCTGCAAGCTCATCAGAGTCACTTCTTCATCCTCATCCTTTGGTGCCTTCTCCCTATTGATGGGATAACAGAGGCTAGGGGTGAGAAAACCCCATTCCCACTTCCATCCCCAGGGGCCCAGGAGAACAGGGACACTGGGCATCTGGGGACTTATGTATGTATGGCAGGAAAGGGGTGGAGACAGATGGTAGGCACCTCCAGGATACAGAGGCCATACACATGCTCGTGTGTGCACACACATGCCACAGTGCACCCCCTACAGTTCCAGCAGCCCAAACACAGGAGAATGCATGCCCCAGTGTCCTGTTCTCAGCAGGGCCCAAAATCAGGGTCTGGGTTGGTGGGGGCAGACCATGGCCATGACCCCCTATGTCCTGGGCCAGTCCCCTTTGACCTGGGGAAACTCTTCCACCTTGGCACAAAGCTCCAGCTCCAATGCCCTAGGGGGGTTTGGGCCCTGGTGGGGGAAGGGGCTGAGGCTGGTACCCCTTCCCCAGCATCCCCAGCCCCACTGAGGCCCTGCCCGGCCCGTTCCAG
Seq C2 exon
ACCGCGGGACAGTGCAGAAGGTCATTGTGCTGCCCAAGGATGACCAGGAGTTGGAGGAGCTCATGCTGGAGGAGGTGGAGGTCTTCAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000001617-SEMA3F:NM_004186:13
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.147 A=NA C2=0.033
Domain overlap (PFAM):
C1:
PF0140314=Sema=FE(15.6=100)
A:
NA
C2:
PF0140314=Sema=FE(6.1=100)
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:
TGCCCTGGTGGAACCTTCA
R:
TTGAAGACCTCCACCTCCTCC
Band lengths:
311-939
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
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)