HsaINT0147472 @ hg19
Intron Retention
Gene
ENSG00000167680 | SEMA6B
Description
sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6B [Source:HGNC Symbol;Acc:10739]
Coordinates
chr19:4546404-4548185:-
Coord C1 exon
chr19:4548039-4548185
Coord A exon
chr19:4546482-4548038
Coord C2 exon
chr19:4546404-4546481
Length
1557 bp
Sequences
Splice sites
5' ss Seq
GAAGTGAGT
5' ss Score
7.97
3' ss Seq
CGGTCCCTGGTCTGCTCTAGGAA
3' ss Score
8.99
Exon sequences
Seq C1 exon
GTGTGGACGGCCCGGCGGTGGCGAGACAGGGCAGCGGCTGCTGAGCTTGGAGCTGGACGCAGCTTCGGGGGGCCTGCTGGCTGCCTTCCCCCGCTGCGTGGTCCGAGTGCCTGTGGCTCGCTGCCAGCAGTACTCGGGGTGTATGAA
Seq A exon
GTGAGTGTCCACCCCAGGCCAGCCGTGGGCGGGAAGCAAGGGAGGATGGGCACAGGGAGGGACAGCTGGGTTCCAGTCAAAAGCCCAATGATGTCCTGGTCATTGAGCTGGGCAGAGGGCATGGCCCGTGCAAAGGCCCGCGGGCAGGACCACTCCTGGTGTGTTGGAAGAACAGCAAGGTGGCCGGTGTGGCTGGAGCACAGTGAGCAAGGGGGAGTGAGGGAGGAGGGGAGGACGGGGAGGGGATGGGAGAGGACGAGGCAGTTTGTGCAGAGCTTTGTGAGCCTCGGGGAGGACTTGGGCTTTGACCTTGAAGGAGATGGGAGCCATGTAGGGTTGCAGGCAGAGGAGGGACTGGCCCTGACTCAGGTGCTTACAGGTGCCCTCTGGTGGCTGCTGCCAGGAGGAGACTGCAGGGGAAGGAGAACCAGGGACCAGGGTGGAGGCTGTTTCCCCGTCTCTAAAATGGGAGGAAAGCTAGGATGCATGCCAGTGCTGGCACACGCCTGCACTCCATGTGAGCCGTCAATGCGGAGGACCCTGCTTCCTGCCCGCCGTTATTGCAACAATGACCCAGTAGCTCCGAGTCCAAGGGCACAGCCTCTGGCACGATGCCTGGGCTCCCATCTCAGCTCTGCCACTTGGGCAAACATTTACTTTCTGGAGCGTCAGTTTGCTTATCTGTAAAGTGGGGAGTGAACAGTGCCCTGCACACAGATTTGTTCTAAGGACTCCAGAAGTTGCTATTAAGAAGAGGGACTGGGCTTGGTAGCTCACGTCTGTCATCCCAGCACTTGGGAGGCCAAGGCAGGAGGACTCCTTGAGCCGAGGAGTTCGAGACCAGCCTGGGCAACACAGCATAGTGAGAGCCTGTCTCTAAAAAAAAAAAAAATGCAAAAATCAGCTGGGCGTGGTGGCACACACCTGTGGTCCCAGCTACCCAGAAAGCTGAGGCAGGAGGATCACTTGAGCCTGGGAGGTTGAGGCTGCAGTGAACTATGATCATGACACTGTACTCCAGCCTGGGTGACAGAGCATGACCCTGTCTCTTAAAGAAAAAAAAAATTAAATTTTAATTTAAAAAAATTTTTTTAATTTTAAAATAAGAAAACGCCAGCCGTGGTGGCTCACACCTGTAATCCCACCACTTTGGGAGTCCGAGGCGGGTGGATCACTTGAGGTCAGGAGTTCAAGACCAACCTGGTGAAACCCTGTCTCTGATAAAAATGCAAAAATTAGCTAAGTATGGTGGCGCGTGCCTGTAATCCCAGCTACTCGGGGGGCTGAGGCAGGAGAATCGCTTGAACCCGGGAGGCGGAGGTTGCAGTGAACCAAAATCCCGCCACTGCACTCCAGCCTGGGCGACAAGAGCGAAATTCCATCTCAAAAATAACTAAATAAATAAACAACAAGAGCGAAATTCCGTCTCAAAAATTAATTAATTAAAATAAAAATAAAGAGGCAGGTGCTTGGAACAGGGCCCACAGGTCACCATCACCATTGGGGTTGTGTAAGTGACTTGGACACTTGTCCCATTCGGTCCCTGGTCTGCTCTAG
Seq C2 exon
GAACTGTATCGGCAGTCAGGACCCCTACTGCGGGTGGGCCCCCGACGGCTCCTGCATCTTCCTCAGCCCGGGCACCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000167680-SEMA6B:NM_032108:13
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.120 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0140314=Sema=PD(0.1=0.0),PF0143720=PSI=PU(16.1=18.0)
A:
NA
C2:
PF0143720=PSI=FE(46.4=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:
GGTGGCGAGACAGGGCAG
R:
GTGCCCGGGCTGAGGAAG
Band lengths:
206-1763
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)