HsaINT0147482 @ hg19
Intron Retention
Gene
ENSG00000167680 | SEMA6B
Description
sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6B [Source:HGNC Symbol;Acc:10739]
Coordinates
chr19:4550811-4552651:-
Coord C1 exon
chr19:4552434-4552651
Coord A exon
chr19:4550943-4552433
Coord C2 exon
chr19:4550811-4550942
Length
1491 bp
Sequences
Splice sites
5' ss Seq
CAGGTCAGC
5' ss Score
7.16
3' ss Seq
CTTTCATCCCAACCCCTCAGCAT
3' ss Score
5.94
Exon sequences
Seq C1 exon
GTGGTGGTGTCCCGCGTGGCCCGAGTGTGCAAGAACGACGTGGGAGGCTCCCCCCGCGTGCTGGAGAAGCAGTGGACGTCCTTCCTGAAGGCGCGGCTCAACTGCTCTGTACCCGGAGACTCCCATTTCTACTTCAACGTGCTGCAGGCTGTCACGGGCGTGGTCAGCCTCGGGGGCCGGCCCGTGGTCCTGGCCGTTTTTTCCACGCCCAGCAACAG
Seq A exon
GTCAGCGCCCACCAATGGGAGCAAACTGGGAGCATTTGGTGGGCATGGGTAGAGAGGGCCTGTATTCACTCCTCAGGTATGCCCTGGGTGCTAGGTTGGGCACCACTGGATTAGACCTCTGAGAGGCCTCGGCCCCAGGCTGGGGTGGGACAAGCTGACACTGACCCTCTAAGTCCCTTTGGTCAGAACTGGGCCAAAGATATCCTCATCCTCTGCCTTTGGGGAGAGGAGCAGGGAGGGCTTCCTGGAGGAGGGGACATTGGAGCTGGACTTTGGGTGTGAGATGGAGGAAGAGGGAAGGGTGTTCAAAGTTGGAGAAACAGCATGTGCAAAGGTCCTGAGGCTTCAGTGAGTTCAGTATACTTAAGTAATCGTGAGAGAGTCTGTGTGGGAAGGGAACTAGGGGAGAATGCACAACAGGAAAGCAGGGAACTGGTAGGATGGATCAGGCAAGGCTTTGTGGGCTGCAGGCAGAAACTTGGACTTTTTCCCTGAGAGCACTGGGGAGCCATGGAAGAGTGAAGAGCAAGAGGGATGAGATCAGGTTTGCATTTTTTGTTTGTTTGTTTGTTTGTTTGGTTTGGTTTTTTTTTTGAGACAGTTTCACTCTTGTTGCCCAGGCTGGAGTGCAGTGGCGCGATCTCGGCTCACCACAACCTCTGCCTCCTGGGTTCAAGCAATTCTCCTGCCTCAGCCTCCCTAGTAGCTGGGATTACAGGCGTGCGCCACCACACCCAGCTTATTTTGTATTTTTAGTAGAGACGGGGTTTCTCCATTTTGGTCAGGCTGGACTCAAACTCCTGACCTCGTGATCCACCCGCCTCAGCCTCCCAAAGTGTTGGGATTACAGGCGTCAGCCACCGCACCCGGCCAAGGTTTGCATTTTTAAAAAGCCTGCTTGTGGACTGGGCACGGTGGCTTCGCCTGTAATCCCAGCACTTTGGGAGGCTGAGGAGGGCAGATCACTTGAGGTCAGGAGTTCGAAACCAGCCTGGCCAACATGGTGAAACCCCATCTCTACTAAAAATACAAAAATTAGCTGGGTGTGGTGGTGGGCACCTGTAATTCCAGCTACTCGGGAGACTGAGGCAGGAGAATTGCTTGAACCTGGGAGGTGTAGGTTACAGTGACCTGAGATCACGTCACTGCACTCCAGCCTGGGCGACAGAGCAAGACTCGGTCTCCAAAAAAAAAAAAAAAAGCCTGCTGGGGAGTGGGCTCTAACAGTGACACTGGGCAGGCAGGACATCCAGTTAAACAGGGATGGGGGCCTGGACAGGGGTGGCCTCGTAGACCCTGAACTGTGGCCCAATCTGAGATGTTATTCAGGAGGAGTGGCTGCATTCGACAGATGCGGGAGGGACAGGGGACATCTCTGGCCTAGGAAGACTGAAGATTCACTGGCTCCTGCAGACAGAGGCTCCTGCACGCACTTGTCCGAGATGGGGCCTCCCACCGGGCTCACCAAACTCTTTCATCCCAACCCCTCAG
Seq C2 exon
CATCCCTGGCTCGGCTGTCTGCGCCTTTGACCTGACACAGGTGGCAGCTGTGTTTGAAGGCCGCTTCCGAGAGCAGAAGTCCCCCGAGTCCATCTGGACGCCGGTGCCGGAGGATCAGGTGCCTCGACCCCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000167680-SEMA6B:NM_032108:9
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.289
Domain overlap (PFAM):
C1:
PF0140314=Sema=FE(17.1=100)
A:
NA
C2:
PF0140314=Sema=FE(10.5=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GTGGCCCGAGTGTGCAAG
R:
GGGGTCGAGGCACCTGAT
Band lengths:
334-1825
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)