HsaINT0147350 @ 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
chr2:97527474-97529531:-
Coord C1 exon
chr2:97529419-97529531
Coord A exon
chr2:97527632-97529418
Coord C2 exon
chr2:97527474-97527631
Length
1787 bp
Sequences
Splice sites
5' ss Seq
AAGGTAGTA
5' ss Score
5.69
3' ss Seq
GCGCCCCGCTTTTCTCGCAGAAG
3' ss Score
8.62
Exon sequences
Seq C1 exon
GAGACGGCTGGCTGCTCAAGGCTGTGAGCCTGGGGCCCTGGGTTCACCTGATTGAGGAGCTGCAGCTGTTTGACCAGGAGCCCATGAGAAGCCTGGTGCTATCTCAGAGCAAG
Seq A exon
GTAGTAAGTTGGGCCCTATCTGCCACTGTCCCCAGCACTATCCCATCTCACTCTCTCCATCTGGCTGCTTCTCCCAGTTGGGCCTATGTGCTTGGCCAGTGCAGAGTTAGGAACACACACACATGTGGATGCACACCTTGCCTAACTTGGGGTGGGTTCCTGGAAACGAGAATGAAAACAGAATGGAATCTGCACTGCACAGGGCCATTATATATAGCCAGGTCACGGGGCTGCGCTCCCAGCATCAAGCCTTGGCAACTGCTCCCATGTTTCTTTCAGACCCTCCAAGCTGTGCTGTGGTTCTGGCTCTGGCCTCTTCCCTGACCATGCCCCTGTGACCAGACCTCCCAGGCTGTGAGATGTTTATGATGCCCTCACCATGGTGGTTTTCCTTCCAGCCCCCATTTCCGTGACTGTTTCCCTGAAGTGCTTGCATTATACCCTTGTGCAATACTCTTTTTGGTTTTTTTTTGAGATGGAGTCTCACTCTGTCACCCAGGCTAGAGTGCAGTGACGCGATCTCAGCTCACTGCAACCTCCACCTCCCAGGTTGAAGCTATTCTTATGCCTCAGCCTCCTGAGTAGCTGGGATTACAGGTGCCTGCCACTATGCCCAGCTAAAGGTTTTTTGTTTTTGTTTTTGTTTTCTTTGAGATGGAGTCTCACTCTGTCGCCCAGGCTGGAGTGCGGTGGCATGATCTCTGCTCACTGCAACCTCCACCTCCCGGGTTCAAGCAATTCTGCCTCGGCCTCCCAAGTAACTGGGACTACAGGCACGTGCCACCATGCCCAGCTAATTTTTTTTTTTTTTTTTTTTTTTGAGATGGAGTCTCGCTCTGTCACCCAGGCTGGAGTGCAGTGGCGCAATCTCGGCTCACTGCAAGCTCTGCCTCCCAGGTTCACACCATTCTCCTGCCTCAGCCTTCCATGTAGCTGGGACTACAGGCTCCCATCACCACGCCTGGCTAATTTTTTGTATTTTTAGTAGAGACGGGGTTTCACCGTGTTAGCCAGGATGGTCTCGATCTCCTGACCTTGCGATCCGCCCGACTCAGCCTCCCAAAGTGCTGGGATTACAGGCGTGAGCCACTGCGCCTGGCCAGCCGGCTAATTTTTGTATTTTTAGTAGAGACAAGGTTTTACCATGTTGGCCAGGCTGGTCTTGAACTCCTAACCTCAAGTGATTTGCCCACCTCAGCCTCCCAAAGTGCTGGGATTCCAGGCATGACCTGCTGTTCCTAGTTGCCTTGTGCAATACTCTTGTGGCATGTTTGCTACACCTCCTGAACTTTGATTTGTTTGCCTTTTACCAGCTATTATGACTCAAAATTGTCCCCTAGAACATGGAATAATGGCAGAAAGAAAGTGTGTGGTTGAATAAACACACAGATTGGCATCCACCGTTGAAACAGGAAAACATCTTATGTTATGCTGCTGCTGTTGTGAGGGCTGATGGGCCTTGAAATGTATTTCCTGCACTATGTGTGTGTGAGTGTGTGTGATTATACTTTTTGGCCTCACAGCCCCATCATCCCTTTCTAATAACGTCACGTCGATAAGGGGCTTAGGATTGCATCTGGCCTGTGTAAGCCCTCTGAGTTCTGCGGTTCTTAGAGTTCCCTTTTCAGCACTATAGCTCTGCCTTGTTCCCTTGTTCCTCCTTCTGGCGCCCCGTGCTGTGCCCCCTGCAGGAGTCCAAGCTGTCCCCATGCTGCGTTCTGGTCCGGCCGCCCCTCCCGTGGTGTGGCCCTGGCCGACCCCCCTCCTGCGCCCCGCTTTTCTCGCAG
Seq C2 exon
AAGCTGCTCTTTGCCGGCTCCCGCTCTCAGCTGGTGCAGCTGCCCGTGGCCGACTGCATGAAGTATCGCTCCTGTGCAGACTGTGTCCTCGCCCGGGACCCCTATTGCGCCTGGAGCGTCAACACCAGCCGCTGTGTGGCCGTGGGTGGCCACTCTGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000168758-SEMA4C:NM_017789:12
Average complexity
IR-C
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(8.6=100)
A:
NA
C2:
PF0143720=PSI=PU(38.0=66.0)
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:
GAGACGGCTGGCTGCTCAA
R:
CAGCGGCTGGTGTTGACG
Band lengths:
247-2034
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)