HsaINT0147496 @ hg38
Intron Retention
Gene
ENSG00000143434 | SEMA6C
Description
semaphorin 6C [Source:HGNC Symbol;Acc:HGNC:10740]
Coordinates
chr1:151142504-151144434:-
Coord C1 exon
chr1:151144385-151144434
Coord A exon
chr1:151142676-151144384
Coord C2 exon
chr1:151142504-151142675
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:ENST00000368914:2
Average complexity
IR
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
Other Skipping Isoforms:
Associated events
Other assemblies
Conservation
Mouse
(mm9)
No conservation detected
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