HsaINT0147495 @ hg19
Intron Retention
Gene
ENSG00000143434 | SEMA6C
Description
sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6C [Source:HGNC Symbol;Acc:10740]
Coordinates
chr1:151104163-151106921:-
Coord C1 exon
chr1:151106877-151106921
Coord A exon
chr1:151105994-151106876
Coord C2 exon
chr1:151104163-151105993
Length
883 bp
Sequences
Splice sites
5' ss Seq
ATGGTGAGT
5' ss Score
10.13
3' ss Seq
TCCTCCCTCTCGGTCGGCAGGCG
3' ss Score
8.22
Exon sequences
Seq C1 exon
ATGGAGCTACTGGGAGTCAGTCTGGCCCTGGGGATTCTGCTTATG
Seq A exon
GTGAGTCCTCTTGTCCCAACCTCACCTTCCCTTGCTCAGCCCACATACCTGAGTGTGTGTCCTGTAGCAGCAGCAGAGCAGCATTCTGAATACCCTGGGAGTATCGGAAAAGGGTCGGCATCCTCCAGATACCCAGCATGTAGCTCAGTACTTGGCACACAGTAGGGTACTTTTTGAACAAATAAATCAATGTCCTGCATGATGAGCCCTTCCCCAGGCCCAGAAGAAACTAGAGGCTGGCGTTCTGGACTCCTGGGTTCCACAGGAGGGAGGAAGGACCCCTGGAAGGGTGTCAGGGGTAGAGATCAAGAGCCTCACTGGCTCTGACCTGGTCTCTGCCACCAGTGCTTCCGGGTCCTGGCCCTTCCCCTGGGACCCCCAGTCCTCCCAGTGATGCCCACCCCCGGCCCCAGTCTTCCACTCTTGGAGTTCACACTCGGGGTAAGGGGGCTACTTGGGAGAGATAGGAGTGAAGTGTGGGGCTGCTGATTCTCGGAGCGTTCTAAGCCCCTCACTGAATGGTGTTTGGTGCTCACTAACGCCTGTTTGGAGCCTCCCTTCCCCAGAATTGGGCATCCCAGCCCCGAGTTCTCCTGCACGAGCAGTTTTTGGCAGTTGCTCTTGGCATGGCTACAGGGGCCAGAAGTGGGATGGGGAATCCCCAGGCCCAAGCTCTGGCCTGAGTGTGAGGGGTAGTGCGTGGGCTGTATGCTGAGGAGTCAGGAGAGGTGAATCCTGAGGATGGTGGAGGCTGTAGGAGTGAGGCTGAGTAGCAGCGGGAGGGACGATGATGTCAGGCCTGGGAACTGCCGGCGCCTCTGGGCCTAGGTACCCCGCACCGCCTCCCCTTGGCTGAGCCTCCCTCCTCCCTCTCGGTCGGCAG
Seq C2 exon
GCGTGCGCCGGGACCTGCCCCCAGCCTCGGCCTCCCGCTCCGTCCCCATCCCACTCCTCCTGGCCAGTGTGGCCGCAGCTTTTGCCCTGGGCGCCTCAGTCTCTGGCCTCCTGGTCTCCTGTGCTTGTCGCCGCGCCCACCGACGTCGGGGCAAGGACATCGAGACTCCGGGGCTCCCGCGCCCTCTCTCCCTCCGCAGTTTGGCCCGGCTCCACGGTGGGGGCCCAGAGCCCCCGCCGCCCTCCAAGGACGGGGACGCGGTGCAGACGCCGCAGCTCTACACCACCTTCCTGCCGCCTCCGGAGGGCGTGCCCCCGCCGGAGCTGGCCTGCCTGCCCACCCCCGAGTCCACGCCGGAGCTGCCGGTCAAGCACCTCCGCGCCGCCGGGGACCCCTGGGAGTGGAACCAGAACAGGAACAACGCCAAGGAGGGTCCGGGCCGCTCACGGGGCGGGCACGCGGCGGGCGGGCCCGCGCCCCGCGTGCTGGTGAGGCCACCGCCGCCCGGCTGTCCCGGGCAGGCCGTGGAAGTCACCACCCTGGAGGAACTGCTGCGCTACCTGCACGGCCCGCAGCCGCCCAGAAAGGGGGCCGAGCCCCCCGCCCCTTTAACCTCGCGGGCGCTCCCGCCGGAGCCCGCCCCCGCCCTCTTGGGCGGCCCCAGCCCCAGGCCCCACGAGTGCGCCTCGCCGCTGAGGCTGGACGTGCCCCCCGAGGGCAGGTGCGCCTCTGCCCCCGCCCGGCCCGCGCTCTCCGCCCCCGCTCCCCGGCTGGGCGTCGGCGGAGGCCGGAGGTTGCCTTTCTCCGGCCACCGGGCCCCCCCTGCCCTGCTCACTCGAGTCCCCTCGGGAGGTCCCTCCAGGTACTCCGGGGGTCCCGGGAAGCACCTCCTGTACCTGGGCCGGCCCGAGGGCTACCGGGGCCGCGCCCTGAAAAGGGTGGACGTCGAGAAGCCCCAGTTGTCCCTGAAGCCTCCCCTCGTCGGGCCCTCCTCCCGCCAGGCCGTCCCGAACGGCGGCCGTTTCAACTTTTAAAGGGAGCGGCCCACGGCCTCCAGCGTGGGGAGCGCCCGAGTCCTCTCGGCCACGAGCTGGACGCTCTTCAGGACGTTTCACCGCCCCCTCGCCCCGCACCTCCAGCCTTCCCGACTCGCAGAGTCTCCCGAGGCCCCTTTTCGCCTCGGGTTTATTTATTGACTGTCTTTCCCCCTGTCCTCGACAGAAGAGTGGGAGGTGAGAAGCCCGTCTCCTCAGTGAGCCAGCATTTCAGGGGGAGCTGGCGGACTCCCACTCCCCGCTCCCTTCCAGCCAAGCTGCCTTAACTCGCCCCTCGGGGCTCCCCCAGAGACTGTGCCCCGGGCGGGCCGCGCGCGCTGTGTCCAGAGTCCTCGGGCCTTCTGGGTCTGGGACGTGCCTCTCCTACTGTGTAGGAGCCTCCGCTTCCCAATACAGCCGTGTCTGCAGCCACTGCCTGACTTCACTCGGGCGGGGGAGGGCGGCAGTCGGTCGGCTCGCTCTGGGCGCCCTCGCTCTCTGCCTTCATCTGGGCCCTGGGCTCTCCCGGGTAATGGGATGGCTGCGGTCCCGCCGGGGGGCAGTCTGGAAAGGTTTCCTAAAGGAGACGAGCGAATTAACGGTGTCGAGGTGAGCCAGGGCCAGGGGGACCCCGGTAAAGTTTAGTTGAGGCTGGGGAAGGCCCTCGGAGCTCGTTTCCAGATCGAGGTAAGAGGGACTTTCTTAAAGGCCTAGTCTATGGGATGGGGCGGCGGAGGGAATTTTTTGAGAAATAAAATGAAGCTGCAGTGTACGTTACTTGAAGTTCCACATCAGAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000143434-SEMA6C:NM_030913:18
Average complexity
IR-C
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=1.000 A=NA C2=0.877
Domain overlap (PFAM):
C1:
PF0143720=PSI=PD(11.3=43.8)
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Associated events
Other assemblies
Conservation
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GGAGTCAGTCTGGCCCTGG
R:
GGAGGCGGCAGGAAGGTG
Band lengths:
334-1217
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)