HsaINT0147496 @ hg19
Intron Retention
Gene
ENSG00000143434 | SEMA6C
Description
sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6C [Source:HGNC Symbol;Acc:10740]
Coordinates
chr1:151114980-151116910:-
Coord C1 exon
chr1:151116861-151116910
Coord A exon
chr1:151115152-151116860
Coord C2 exon
chr1:151114980-151115151
Length
1709 bp
Sequences
Splice sites
5' ss Seq
CAGGTAAGG
5' ss Score
11.08
3' ss Seq
TTCCCTGTCTCCCCTTTCAGGGC
3' ss Score
14.37
Exon sequences
Seq C1 exon
GTCAGAGGTTTCCTATCCCCCTCAAGCCCCCACAGGAGTCACCAACCCAG
Seq A exon
GTAAGGAAAGGGCAGCAGCTCCTGAGGGCAGGGGGTGGAAGCAGGCATGAGCAGGGAGCAGAAAGAGGGGCTGGCTCTTCTCCTCACTTGCCAGAGACCAAAGTTGTTTCCAGGGTGAAGATACCAGTTGCTCAGGGCAACTTGGAGGCAGGGGGGTGGTGGGGAGAGCAGGTTGGGGAGGATGAGAGACAAGCTACGTCCCTTTCTCTTCCCCTGGGAACAACAGTATCCGGAAACATGTCGGGGGAGGGAGGAAGGCCCAGCCTTTCAACACCAGAGGGTCGTTAGCTAGCTGCTACTCTGCCCTGGGGAAGGGGGGTCATCATTAGGTGTTCCTACTCTTTTCCTTTCTTCAGCTCTCTTGAGGCCCCACCTGACGTCAGCCTCCCCACCAGTGATGCTGGATTGGGGGTGGGGGGACACTTGGGTCCTGGCTGGGAGAGTAGAATTACTGGGGAGATGGAAGGGGGCTTGGCCTGGAAGCTTAGGGTCTGTTTTAGGGGACACGGTGGGATGGGCAACTAAGGATTGGTGAAGGATAGTTATCTGTTCACAAAAGAAAGGAGTCTCACCCTTCTTGACCTGATTTTTGGAGCCGACCAAGTCCCTCACTTCAATTTTAGGGGAAGGCAGGAAGCTGGTGTATACCTCCTGCTGTGGGCCCCAGCCAGGGTCATTTGGCTGAGGGAGGCTGATGGTGGAAGGAGACCTGTCTCACCATCTCTTCCACCATATCCATCTTTTCCTGGACTTTGGGCTACAATTACCTGCCTGTCACTGAATAATTTATATTTTAATTTCAGAGGCAGCAGATGAGGGAAGGAAGGGAGAGAGGCGCACGTTTAGCCATTTTGCTTCACTAGTCCCTTGTACCCCTGGCTTCTCATAGGGGGTGGGTCTGCTCTTCCCCCCTCAAGTACATGCACTGGTTCTTAGGAGCCAGGGAAGGAGCAGGGGGCTAGAGAGCCTGGAGGGGGTGGCACAGTGGTCGGGCAGACAGCTGCAGCCAGAGCTAAATTTAGCCTCTGATCTGGCTTTGATGCAGATTCATTTTTGGCGAAGACAGTCCCCCCCACCAACTCTCCTCCCTACTCAGTTCTTCCCTAGCGGTGGGAAGGGCCCCTGAAGCATGAGCTTAGACCAGCACAGTGACCTCTAGGCTGCCTCCCCCAACTGTGTCTTCCTCAACTCTAGAAAGGACAGTGTCAGCCACACGGCTGCCCCCGCCTAGGCGCAGTGCCTGCATTGCTCCCAGGGTGCCGTGGGGGTCTGGGAGGGAGGGGGAGTCAGACATGGTGCCCTTTTCCTCCTCCCAGTGCCAAGGAGTCACTATTTATAATTTTAAGGCTTCAGTCTCTAATTATAGCTGAGAAGGGGTTAGCAAGAGGGGGGCCAGGAGGTGTCACCTACTGAATGTCCCAGACCCAGTCAGGAGAGAAGAGGAAAAGCTGAGATGGGGGTGGGTGTGTCCTGTCCTTACCTGGGGTCATGCAGGCAGGCCTCACACCAGCCAGTTTGGGCCAGTTGCAGAGGGAAGGGCCTTGAGTGACAATGACAGCTGGCTGGAACTGGGGCAGTGCTGGAGAGAGGGTTCTTTTCCCCCACCCCACAGGGTCTTCTGGGGATACACCAGGAGAGGAGCCTGCTGGCTTGCTTCAGGGGAGAGGGAACTTCGCTCCTCCCCCACTTTTCCCTGTCTCCCCTTTCAG
Seq C2 exon
GGCCGGCTTATGGGTGAGGGGGCACCCCCTGGGGCCTGAGCTGCCCCGCACAGGATGCCCCGTGCCCCCCACTTCATGCCCTTGCTGCTACTGCTGCTGCTGCTCTCACTTCCCCATACTCAGGCCGCCTTTCCCCAGGACCCCCTCCCTCTGTTGATCTCTGACCTTCAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000143434-SEMA6C:NM_030913:2
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 Inclusion Isoform:
NA
Main Skipping Isoform:
NA
Other Inclusion 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:
GTCAGAGGTTTCCTATCCCCCT
R:
CTTGAAGGTCAGAGATCAACAGAGG
Band lengths:
222-1931
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)