HsaINT0145229 @ hg38
Intron Retention
Gene
ENSG00000139697 | SBNO1
Description
strawberry notch homolog 1 [Source:HGNC Symbol;Acc:HGNC:22973]
Coordinates
chr12:123309489-123309856:-
Coord C1 exon
chr12:123309710-123309856
Coord A exon
chr12:123309584-123309709
Coord C2 exon
chr12:123309489-123309583
Length
126 bp
Sequences
Splice sites
5' ss Seq
TAGGTAAGT
5' ss Score
9.66
3' ss Seq
GTTTCTTTTTCTTGTTCAAGATC
3' ss Score
7.14
Exon sequences
Seq C1 exon
ATTATAACAACATAGGAAAATTCTTAAATAGAATTTTAGGCATGGAGGTGCATCAGCAGAATGCGTTATTTCAGTATTTTGCGGACACACTTACTGCAGTTGTTCAAAATGCCAAAAAAAATGGAAGATATGATATGGGAATCTTAG
Seq A exon
GTAAGTAGGGAAAATTTCCCCCCCACAATGTCCCCAGGGAAAATGTGGAGTGGAGAAATTCTTTAAACGTGTGTACCTGATAAAAATGTTCTTTTTACATTTACATGTTTCTTTTTCTTGTTCAAG
Seq C2 exon
ATCTTGGTTCTGGAGATGAAAAAGTGCGGAAAAGTGATGTTAAAAAGTTTCTGACTCCAGGATATTCAACCTCTGGCCACGTAGAATTATACACA
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000139697:ENST00000267176:26
Average complexity
IR
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:
PF138711=Helicase_C_4=FE(17.7=100)
A:
NA
C2:
PF138711=Helicase_C_4=PD(0.1=0.0)
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:
TAAATAGAATTTTAGGCATGGAGGTG
R:
TGTGTATAATTCTACGTGGCCAGA
Band lengths:
218-344
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