HsaINT0147486 @ hg19
Intron Retention
Gene
ENSG00000143434 | SEMA6C
Description
sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6C [Source:HGNC Symbol;Acc:10740]
Coordinates
chr1:151116861-151119140:-
Coord C1 exon
chr1:151118909-151119140
Coord A exon
chr1:151116911-151118908
Coord C2 exon
chr1:151116861-151116910
Length
1998 bp
Sequences
Splice sites
5' ss Seq
GGAGCAAGT
5' ss Score
0.81
3' ss Seq
TTTGTCCTGTCTTCCATCAGGTC
3' ss Score
12.37
Exon sequences
Seq C1 exon
ACTGGGGCCGAGCCCAGAGCCCCGGGCGGTCGCATTGTTTTCCTCCGCGGATCCGCGGCTGGACTTGGACCCAGGGCTCTCCCGACAGCGCCCTGGAACCCAAATTCAAGCACCATCCAATTCGGACGCTCATCGCATCTCGCCTGAGCACAACCACGGATTGCGAACTCAGCGCAGCGCGTGGCCGCTGGCCGCCCGCGGCGATCTCGATCCCGCTGACCCGAATCCTGGA
Seq A exon
GCAAGTACCCCGGGCAGGGAAGGGGCTGCGGGGAGGCGGGGAGGGAGCAGGAGGGCGCGGCCGGCGGGGGGCAAGCTTCTGAAGCGCTAGGGGACCAGGGAGGTGTCGGCGCCCGGTGTGCCTGGCTGACGGAGAGGGTCAACGAAATTGGGGTGCAGGGAGGAAGGAGGGACAGTGGCCGAGCCCCGTAACTGTACTGGTGAGAGCAGAGTCTGGGCACCTCGTTCAATTGGGCTTTCGTCGAGTCGCATCCCGCTGGACTGGGAAGCGCGAAAAGGGATTATTTGAGGCGCGCTCCGTAGAGAGCGTGGAAAACCTGGCCCCTTGCTTTCCCAGCAAGGAAACTAGGGCTCCGAGACCCACGGAGAACTAGACCCTCCTGACGCCCCTGAAGGGATGGGAAGAGGGACGCATCGTTCCGGACTTTGTGTCACGGGTGCTCCTCTGTCCTTGTGCAAGCCGGAATCTGAGCACCCTCTGAAGGGTTGGCTCGTGCAAAGAGGCGGCGAATGGGGCCCTCGAGCAACATCGGTCCCAGCGCCTATCTCCTTCCTTCAGCCCGCTCGGCCCGGGGCTTTGTTAGACTGAGGTCTCCCAAGGAGGACATCCGAGCTGGCAACTGCCTCCTGAGCCCACGGTCCCCACTGAGCGCCGGCCTCAGGCCCGCCCTCGTCGGTTCTCAGCCTCTGGCCCTGTTTCCCTGGCCTGGGAGACCCGCCTCCGCTCCCCAACCCCCGCTCCTATCCCCTCTTCGTCTGCGCCTGCAGGCCCCTCCAGCCCCTCCTCTCGCTAACGTGGCTCTGGGACCCGGTCCCGGCCCAGACTCTGCTACCGGCCCCTCCTCGGAGCCCCGGATCCGGTGAGGGGGAGACAGGTCGAGCCCCTGGCCCTAGGCCCACCTCTTTTCGAGGCTTTAGACACCTGGATTGTCCTGGTTGGGGGTTGGGTGGGAAGGAGGGTAGGTGCTGAGTGTGGGGCTAAGAGCTAAGAGTGGGGGAAATGGCTTGGAGAAAGGAAAGCTCCGGTTCCACAGGCTCCTTGGCGCGACCCTGCTCCCTCTGAGGAAGGTGGACTGGGGCGGGCGACCAGCCCAAAGGCTTCCTGCTATTGTCCCCAGCCCAGTCTCCCCTTCTCCATCCCTTCCACAGCTCTCCTAGACTCTGGCTGTGACCCCAGCCATTCCCCAGAGGTGGCTTCGGGGCCAGGAGAGAGAAGGGCTGTTTCCTCTTCCCAGCAACGGGAGGATCTGGAAAGGGGAGAGTCGGCCAGGTCTCTCCCATGTGCTTCAGATGGGGTGTGTGAAGCAGCTCGGATTCTTCCAGGGCAGAGTGATCTTTTCTCCAGGCCAGGAGTTGAGGAGCTGACCAGATGCTGCTTCCCAGAAACAGCTACAAGAAGCCCTCTTAAAGGTGTATCATAGTTGAGTCTAGAAGGCCAATGCAAAGGCCAGCCAAGTGTTTGTAGAGGCTGGACTAATCCAGCCTAAAGTGGGGTGTGAGTGTGTGTGTGTGTAGACTGAGTGGAAGGGAGGCACAGCCTGCTCTCTCAGGGAGGAAGGAAAGGGTTGAGGGTGCTTGCTATCAGATCATTTTGCCTGGAAATGAAGAGCATGTAAATGAGATGCAAATTAGCCTCTATTGTCCCTAGCTAAGGCGCTTTTGCTAAGAAGGCTGTTGGATTCTGAGGGCCTTAACATGGGAGTGGTCGCCATGCCCCACAAACTCTCCCAGTGACCCCCTTTGCCAAGGCTAGCCCTGTAGTTCTAGCAGTTTCTAGAAAGGGGCCATCCCCTTCCCCTGCATCTCTGGGCATAAAGCCACCAGCACCTTTGTAACCAAACTATTAAGAAGTGTCATCAGCCCCCTCCCATTTTCAAGGCAGCATCTCCCCTACCCAAGCGTCAGCAGACTTTTCTTGAATTTTTACATTTACTTGTAAGGGATGTGGTAAGGGGAGCATAATGCAGTCTCTTCTCTCCTTTGTCCTGTCTTCCATCAG
Seq C2 exon
GTCAGAGGTTTCCTATCCCCCTCAAGCCCCCACAGGAGTCACCAACCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000143434-SEMA6C:NM_030913:1
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
5' UTR
No structure available
Features
Disorder rate (Iupred):
C1=NA A=NA C2=NA
Domain overlap (PFAM):
C1:
NA
A:
NA
C2:
NA
Main Inclusion Isoform:
NA
Main Skipping Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CGGTCGCATTGTTTTCCTCCG
R:
CTGGGTTGGTGACTCCTGTGG
Band lengths:
256-2254
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)