HsaINT0147349 @ hg19
Intron Retention
Gene
ENSG00000168758 | SEMA4C
Description
sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4C [Source:HGNC Symbol;Acc:10731]
Coordinates
chr2:97529419-97529885:-
Coord C1 exon
chr2:97529663-97529885
Coord A exon
chr2:97529532-97529662
Coord C2 exon
chr2:97529419-97529531
Length
131 bp
Sequences
Splice sites
5' ss Seq
CAGGTGGGT
5' ss Score
8.56
3' ss Seq
TTCTCCTCTGCACCCCCCAGGAG
3' ss Score
7.85
Exon sequences
Seq C1 exon
TGCATTAACAACTGGCATCGGCGCCACGGCTACACCAGCTCCCTGGAGCTACCCGACAACATCCTCAACTTCGTCAAGAAGCACCCGCTGATGGAGGAGCAGGTGGGGCCTCGGTGGAGCCGCCCCCTGCTCGTGAAGAAGGGCACCAACTTCACCCACCTGGTGGCCGACCGGGTTACAGGACTTGATGGAGCCACCTATACAGTGCTGTTCATTGGCACAG
Seq A exon
GTGGGTGCATGGGTATGCAGGCATGGCTGCTCAAGGCTGGGCAGAAGCCCGTGTGCCCAGGGCAGGGAGATTTGGAGCTGCCCCACGGCCTTGTGCCCTCTCATTTACACCTTCTCCTCTGCACCCCCCAG
Seq C2 exon
GAGACGGCTGGCTGCTCAAGGCTGTGAGCCTGGGGCCCTGGGTTCACCTGATTGAGGAGCTGCAGCTGTTTGACCAGGAGCCCATGAGAAGCCTGGTGCTATCTCAGAGCAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000168758-SEMA4C:NM_017789:11
Average complexity
IR-S
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(17.2=100)
A:
NA
C2:
PF0140314=Sema=FE(8.6=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AGCTACCCGACAACATCCTCA
R:
CTGCAGCTCCTCAATCAGGTG
Band lengths:
242-373
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)