HsaINT0147353 @ 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
chr2:97532020-97533660:-
Coord C1 exon
chr2:97533515-97533660
Coord A exon
chr2:97532169-97533514
Coord C2 exon
chr2:97532020-97532168
Length
1346 bp
Sequences
Splice sites
5' ss Seq
GGGGTGAGT
5' ss Score
7.93
3' ss Seq
AGCCATGCTTACCCCTGCAGAGC
3' ss Score
6.84
Exon sequences
Seq C1 exon
GACAGCTGGCCTGAAGCTCAGAGCCGGGGCGTGCGCCATGGCCCCACACTGGGCTGTCTGGCTGCTGGCAGCAAGGCTGTGGGGCCTGGGCATTGGGGCTGAGGTGTGGTGGAACCTTGTGCCGCGTAAGACAGTGTCTTCTGGGG
Seq A exon
GTGAGTGCCTGGAGGGGTGAGGAGGAAGTCAGGGACAGGCTGCTGAGGAGTTGCCCCCATAGTGTGCTGGCTTTATTCTCACGTGTGTGGCACAGCTTTCTAAGAAACTCGAGTTGGAAGAACGGGCAGTGTGGGTTGGGACCTGGGATTAGCCTCCTCTGGGGGAGCTCTGTCCAACTCCCCACCCCAGACTGCCTGCCCAGGTGTGGGAGGGGGAGAGCCTTCTGCCTCGCCCTCTCCACGCCTCGCTTCTTGAATTGTCACTGGCGCTGGGAGCCTAAAGAGAAACTGGAACCGGGATAAATATAAACTGGAGGCTCTCTCCCCTGGCTCCCCAGGCCCCCCTAAGACCTCCTACTGCCCTGTACACATCATACACTCTGGTGGCCCTGGAAGTGTGTGTGTATGTGCACATGCTCGCATGGTTGCCGGGGCACAGCGGGGACCCAGCAGTGCTCCCTGTGCACACACCCGTGTGAAAGGTGATGTCAGGTGTTTGTATCAGCCGTGCGCTCTGGGGACCTGGGATGAGCTCACCTCCCACAGGCTCCACTCGGGTGCCAGTGAAGCCCTGCCATGCCGGTCTGTGTCTGGATCCATTGTTGCCTGCAAAGACTAAGGCTGGTTTGGGGGGACCCTGAGGACAGGTCGGCAGCCATATTTGGCAGCTGATGTAGGAATCACGTGACTGTATAAATGTCGTAGTGCCCTGCATGCCGGGTGGCAGCAAGACTTCCCAGGCCCCAGCCCCATCTCCGCTCTCTGAGCCTCTGGTTTCTCCGGACCTCCCTGGCCTGGCTCACAGCCCAGCTCCCCTCCTGCCATCCCCACCTGTCCTAGTGGCCTGCTGTGCTCGCATCTCTGGCAGCCTGGATTGGGGTCCTGCTGGAGTGAAGGGTTTCCTGAGGCAGGGAGTACTCATAGCCGTCTGTGCCTCCTGCTCTGCTGGACTCTGATAGAGGCAGTGGGCAGCAGGGCAAAGAAGGAAGCAGCCGCCGAGGAAGCGAAGGTGGGGTGGGGGTGCCCAGCCCTGCGGCCGGAGGTGCCATTGACCCTGAGAGCAAGAGCCATCAGTCTGATGGCTTCCTCTGGCCGGAAGCTGTGGCTGAGATATCCTTCCTTCCTCCCAGCAGCCTGGATTTGCCTCCTCCCAGGCTGGGAAAGGCTAGGGAGGCCCAGGTGGGGCTGTCAGGGCCAAAGGCTGTTTCAAAAGTGTCCTTTATTGCCAATCAGGGGGTTTGGCTGGCATCTGCTTGTGGCATGGGGTGCTGGCTCTCGTGGAGCAAGACTGAGGGCTGTCGAGCCCCAGGGGTCCTGCCCATCAGCAGCCATGCTTACCCCTGCAG
Seq C2 exon
AGCTGGCCACGGTAGTACGGCGGTTCTCCCAGACCGGCATCCAGGACTTCCTGACACTGACGCTGACGGAGCCCACTGGGCTTCTGTACGTGGGCGCCCGAGAGGCCCTGTTTGCCTTCAGCATGGAGGCCCTGGAGCTGCAAGGAGCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000168758-SEMA4C:NM_017789:2
Average complexity
IR-C
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0140314=Sema=PU(22.1=66.0)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TGAAGCTCAGAGCCGGGG
R:
CGCTCCTTGCAGCTCCAG
Band lengths:
284-1630
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)