HsaINT0147347 @ 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
chr2:97533515-97535735:-
Coord C1 exon
chr2:97535613-97535735
Coord A exon
chr2:97533661-97535612
Coord C2 exon
chr2:97533515-97533660
Length
1952 bp
Sequences
Splice sites
5' ss Seq
TAGGTGAGC
5' ss Score
7.96
3' ss Seq
CATGTCTTTTCCCTCAGCAGGAC
3' ss Score
9.27
Exon sequences
Seq C1 exon
GGCAGAGAGGCCGCGGAGGGCTGGCGGGCGAGCGCGGGCAGGCGGCGACGCGGGGGCAGGGGTGGACGGCGGTCAGAGCCGAACGCGAGGGCGGCGCCCGGGGACTGGAGCTGCGCGCAATAG
Seq A exon
GTGAGCGAGGCCGGGCTTGCGTGAGGCTGGAGCCGCGGGGCCCCGGAGCCGCCGCTTTGTCCCTTTGCTTGGGCAGGGGCTGCCGGACGCGGGAGGGACAGGGGCTGGGGCGCGGGGAGCCGCGGCGGCGGAGACGGCTGTACGCGGGGATCCTTCCTGCGACCCCCGCGGCTGCTTCGCAGGGTCTCGGGAGTGGGGCGCACAGCACCTGCAGCCCCGCAGCCCCGGGGCCGGAGGGGCGCGCCAGCGAGGGTTCCTCGCGCGGTCCGGTCCGCGGCCGGGATCCTCGCCAGGCTCCTGGACTGCCCTCGGCGCTCCCACCCCCGATGGAAAGTTTGGGGCGGGCTTGGAGGGAGGCCGATGTTGTGGGATCGGATTTCCCTGCCGCGGCCCCCCGCCCGCCCGCCCATTCCGCTGGGGAGGCGGGTTGTCCCGGAAAGCCAGGCCCCCGGGCCGAGCCGGGCCGCGCCGTCCCCGGCTGGAGCGCTCGCCCTGCAGGGAGGGCCGCGGTCCACGGCTGGCCGCTCGGGGTGGGCGAGGGTGTGGGGTGCCCCGCCTGGATCCCGCACCCCTCCCCCCAACCCCTCCTCCCGGCTGCCCGTTTCCTCGCCCTGGGGGGAGCTGCGGGTGGGAGCACCGCTGCCGGGCGGATCCTCGGAGCACGCCACGGGGTGCGGCCCGATCCTCGGGTAAGGAGCCGAGATGAGGCCGCGGGCGTTTTGGGGGGCTGGTCTGGGGCGCAGCCCCCGCTCTCCCGCGCCGGGGCTCTGGGCCGACAGGGGGCGTCCGCAGGCCGGGCTCGCCACGCTCCCCGCGCCGCCGCTTTGTTTGCGTTCAAATCCCTGGAGCTGGGGGAGGGGAGAACCCGGGGGGACCCGGGACGGGGTCTTGGCGGGGACCCTTTGTTTGGGGGTGAGCAGGTCCCCAGCTTCTGCGTCTCCGCCCCTGGCACGGGAAGGCTGGAGCAGGGGAAGCCAATCCCGCTGGCCCGCCCAGGCCAGGGTCCCTGGGGCGCAGTCCCCGAGTTGGGAAGGTTCGTCAGAGTCGCGGGAGCGCAGCGGGTGCCGGCCGTGCGCGGCGCGTTGCCAGCGGCCCGGGAGGAACCCCCTCGCGTCCCCGCCCCTACCTCCCCCCGTCGCCTGCGCGCGCCGCCGGAGTCCCCGACTCGACCCGAGCTCGGTCCCCCCACCGCCCCTCCGCCAGAGGGCTGGTGTTTCGGAGGAGGCAGTGCGAGGAACAGGATGAGGCCCTGGTCATTTCCACGCCCATCCCACCCACTTCCTGCCTCCCTCTTGGGCAACAAAGGGGCCTCGGGAAGCTGGGCCCCTTCGCTCCCGGCCCTTCTCACACTCCTGCCCTGCTGATGTGGAACGGGGTTTGGGGTTCTGCAGGGCTATTGTCTGCGCTGGGGAAGGGGACAGGCCGGGACCGGGACCTCCGCTCGCAGCCGGCCGCACCAGGTTTCCCCTTTGGGGCTTTCCCGACCGCCTACCCCACCGCATGCCCTCGTCGCCCTAAGGAGTCTTCCTCCCAGAATTAGGTGTTGGCAGGGTCCGGAGCCCCAGTGGCTGCAAGGCCTGCTGCCTGAGGTTCTTTCAAGAAACTCAAACCTCTTAGGCCTGAGTGTGTATGTTGGGCGGGGGTCCCCTTTTTATTTCTCAAATGATTTCCTGTTGCGCAGAGGTAGTGGTGGGTCTGGAGGCCAGGGAGGGCTTCCCGGAGCCTGTTTAGCCTTCAGCCAACTCAACTCCTCCCCGCTTCCCAGGGAGACCTGTGGTCTTTTAGGCAGAGGCCAAGTGTGGGGACTTAGGTCCACCTCCAAAGAGAAGGGGAAGGAGGGCACCGGGGCTCCTGGAAGGCCTGATGAGGAGTCCTGTGGCCTCTCCTGCTGCGGGCCCCTCTGGTTTGCTTTCTCTGGCTGTGATTTCTGACCATGTCTTTTCCCTCAGCAG
Seq C2 exon
GACAGCTGGCCTGAAGCTCAGAGCCGGGGCGTGCGCCATGGCCCCACACTGGGCTGTCTGGCTGCTGGCAGCAAGGCTGTGGGGCCTGGGCATTGGGGCTGAGGTGTGGTGGAACCTTGTGCCGCGTAAGACAGTGTCTTCTGGGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000168758-SEMA4C:NM_017789:1
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
5' UTR
No structure available
Features
Disorder rate (Iupred):
C1=NA A=NA C2=0.000
Domain overlap (PFAM):
C1:
NA
A:
NA
C2:
NO
Main Skipping Isoform:
NA
Associated events
Other assemblies
Conservation
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GGTGGACGGCGGTCAGAG
R:
ACTGTCTTACGCGGCACAAG
Band lengths:
198-2150
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)