HsaINT0147481 @ hg19
Intron Retention
Gene
ENSG00000167680 | SEMA6B
Description
sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6B [Source:HGNC Symbol;Acc:10739]
Coordinates
chr19:4552434-4554488:-
Coord C1 exon
chr19:4554400-4554488
Coord A exon
chr19:4552652-4554399
Coord C2 exon
chr19:4552434-4552651
Length
1748 bp
Sequences
Splice sites
5' ss Seq
AAGGTGAGG
5' ss Score
9.16
3' ss Seq
CCGTCCACTGTCACGCCCAGGTG
3' ss Score
5.7
Exon sequences
Seq C1 exon
AGCCTTACTTTGTCCATGCGGTGGAGTGGGGCAGCCATGTCTACTTCTTCTTCCGGGAGATTGCGATGGAGTTTAACTACCTGGAGAAG
Seq A exon
GTGAGGCCGGTGCAGTGGGGCATGAAGTTGAGAGGCTCTGATCATGCGAAGTGAGGGGGCAGAGGTGGATCCATGAATCCCTGCATGGGGTGAGAGGGTCCTGCCCTCCATTTCTGGTCCCCAGGGCCTCCTTTCCAGCCATGATCAGGCCCTGAGGCTGAAGACATCTACGGAGCAGCCGTGGAGCACTCAGCCCTGACGAGGGACTTGAGTTGGAAGTCAGATACACCTGGTGCTGTTGCTGTTCACCTGTCCACCCACCCACCCAGCCACAATCACTTATCCATCCTTCATCCCCTGTCCATCCGTCTACCTGCTCACCCTCCCACTTACCCATCTGTCTGTTCTTCAGCCCACCCACACTTTCATGAGCCCATTAATCCATCTACTCATCTGCCCACCCACTCACTCATCCACCCACTACCATCCATCCGTGCACTCATCCATCTGTCCATGCATCCATCCACCCATCGATTCATCTAGCCACCCTTCCATCCTATCCATCTATCAGTCCATCCACCTATCCATCCATCTATCCATCATCTGTCCATCCATCTGCCAATCCATTCACCCATCCATTCATCCATCCATCCATCCCATCCACCCATCCATCCATTTATCTACCCATCCACCAACACACCCACCCACCCACCCACCCATCCATCCATCCATCCATCCACACATCCATCCATCCATCCAGCTGCCAATCCATCCACCCATCCATTCATCCATCTACCTATCCACCCACCCATCCATCCATCCTTCATCTATCCATCCATCTGCCAATCCATCCACCCTTCCATCTCATCTATCCATCCATCTCATTCACCCACTCATCATCTATGCACCCACCCATCTATCCATCCATTTATCTGCCCATCCACCCACACACCCATCCATCCATCCATCCATCCATCCATCCATCCATCCATCCATCCACTCACCCATCCAACCATCCACCCATCCAACTCACCTATCCATCCATCCATCCATCCATCCATCCATCCACTCACCCATCCAACCATCTACCCACCCAACTCACCCATCCATCCATCCATCCATCCATCCACCCACTTATCCATCCATTCATTCATCCACTTATTCACCTATCCATGCATCCATCCATCCACTCACCTAGCTTTCTCTCTATCCATCTGTTCATCCATCCACCCACACATCCATCTACTTATCTACCAATTGCTTGATTACCTTGTTCTCCTTCACCATCTCTTCCATTATCTATCATCCTTCTTCAGATGTATTTATTTATCCATCCACCTACTCATCCCTCCATTGTAATCGTCCGTCCATCTACTCATCCACTCATCCGTCCATCCAGGCAACCAGGCAGTGCTGAAGTGCACAGACTGCCACTAACTACTATTGTGACCTTGGACCAGTCACTTCCTTTTATCTGTGCCTCTTATCAGTGTCCCCACATGTACAATGGGGGGATATCAGTAGGCCCCCCTCGGGAAGAGTGTAAGAGATGTGAGAATAAAATGTGGGTCTTCGTGGAAACAGTGATGATTATGGTTGTCACTGTTGCTATTATCATCATTGACATTCCCACCGGGAATTTCTGCCAGGGAAGCCGGTGCCCAGAGAGGAACGGTGACTGGCCGGGGTCCCACCAGAGCCAGGGTCAGACTCCTCCATCACAGTTTGGGTGGTGAGTGGCACAGCCTGTGAACAGGCCTTCCTGGGACACAGAGCTCAGGCCCCCGTCCGTCCACTGTCACGCCCAG
Seq C2 exon
GTGGTGGTGTCCCGCGTGGCCCGAGTGTGCAAGAACGACGTGGGAGGCTCCCCCCGCGTGCTGGAGAAGCAGTGGACGTCCTTCCTGAAGGCGCGGCTCAACTGCTCTGTACCCGGAGACTCCCATTTCTACTTCAACGTGCTGCAGGCTGTCACGGGCGTGGTCAGCCTCGGGGGCCGGCCCGTGGTCCTGGCCGTTTTTTCCACGCCCAGCAACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000167680-SEMA6B:NM_032108:8
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=0.000
Domain overlap (PFAM):
C1:
PF0140314=Sema=FE(14.6=100)
A:
NA
C2:
PF0140314=Sema=FE(17.1=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:
AGCCTTACTTTGTCCATGCGG
R:
CTGTTGCTGGGCGTGGAAAAA
Band lengths:
307-2055
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)