HsaINT0145224 @ hg19
Intron Retention
Gene
ENSG00000139697 | SBNO1
Description
strawberry notch homolog 1 (Drosophila) [Source:HGNC Symbol;Acc:22973]
Coordinates
chr12:123800095-123801903:-
Coord C1 exon
chr12:123801768-123801903
Coord A exon
chr12:123800208-123801767
Coord C2 exon
chr12:123800095-123800207
Length
1560 bp
Sequences
Splice sites
5' ss Seq
TCGGTAAGT
5' ss Score
11.78
3' ss Seq
AAAACAAAATTTCGTTGCAGGAC
3' ss Score
6.35
Exon sequences
Seq C1 exon
AATATTGCTATCATCTCAGAAGCTGCCAGCTCGGGTATTTCATTACAAGCAGATAGGAGAGCTAAAAATCAAAGGCGAAGAGTTCATATGACTTTAGAATTACCTTGGAGCGCTGATAGAGCAATTCAACAGTTCG
Seq A exon
GTAAGTTCCTACAAACTGGATTTCACTTAATGGATAGCTAGGAATCATTGGGGTAAATTTGCGCATACCAAAACCTAGGTTTAGGCCGGGCACAGAGGCTCACGCCTGTAATTCCAACATTTCGGGAGGCCACTGTGGGAGGATAACTTGAGTCCGGGAGTTTGAGACCAGCCTGGTCAACGCAGTGAGACCCTTTCTCCACCAAAAGAAAAGAAAAACAGCTGAGAGCAGTGGCTCGTGCCTGTAATCCCAGCACTTTGGGAGGCTGAGGTGGGTGCATCACTTGAGGTAATAGTTTGAGACCAGCCTGGTCAACATGGTGAAACCCAGCCTCTACTAAAAATACAAAAATTAACTGGGTGTGTTGGCACACACCTGTAATCCCAGCTACTTAGGGTGCTGAGACGGGAGAATTGCTTGAACCTGGGAGGCGCAGGCTGCAGTGAGCTGAGATCACGCTATTGCACTCCAGCCTGGGCAACATAGGGAGATTCCATCTCAAAAAAAAAAAAAAAAAGAAGAAGAAAAGAAAAACTTGCTGGGTGTGGTGGCGTGTGCCTGTAGTCCCAGCTACTCAGGAGGCTGAGGTAGGAGGATTACTTGAGTCCAGGAGTTCAAGGTTGCAGTGAGATATGATTTCACCACTGCACTCCAGCCTGGGTGACAGAGCGTGACCTTGTCTCAAAAAACAAAAACAGGCTGGGCGCAGCGGCTCACGCCTGTAATCCCAGCACTTTGGCAGGCTGAGGTGGGTGGATCACCTGAGGTCGGGAGTTCAAGACCAGGATGACCAACATGGAGAAACCCTGTCTGTACTAAAAATACAAAATTAGCCGGGCGTGGTGGTGCATGCCTGTAATCCTGGCTACTCAGGAGGCAGAGGTAGGAGAATCGCTTGAACCCGGGAGGCGGAGGTTGCAGTGAGCCAAGATCACACCATTGCACTCTACCTTTGGCAACAAGAGCGAAACTCTAACAACAACAAAAAAATCCTGTTTAATGTCTTATATCTTATCTCGAAATCTCAGATCTTGCATTTAAGGAGTGTTATATATATACTTTATAGTATATGATGCATTGTGGATTCATTTTTTGCTTGTTTACAAGTTGTAAAAAATATATATGTGGTGGGAATTTGTGGGGTTCCAAGAACAGGGTTCCTCAAGGAGTGTCCTTATAAAACTTAAGGATGTATTAGGTCCATATCAGAGAAGCTGCTACTTCTATATGTGTTTCCAACCTCAGTAGCTTCACCAAAGGCCCATAGCTCCTCCCTCCATCTTCATGTTCTTGTGACCAATGATTTGAAAAACAATTTTGGGAAAATCCAGAGTAATTGTGCATCAGTAACATGTGGTTAAGCAAAATTGGGGTAGCAATGCTAATACTTCTGTCATTGAGCAGTTTTATGTGTGTTATGGTAATTTTACATTATCTGTAATTTTTATTGTTTAGTGGTTTCCCAATACCAGTTTAGTGTTAAATGCTAGGAATACATCTCAGAATATTCTCTGTCCAGCGAACACAATCAATGATCTTTAAAACAAAATTTCGTTGCAG
Seq C2 exon
GACGTACTCATAGATCAAACCAAGTTACTGCTCCTGAGTATGTCTTTCTGATATCTGAACTGGCAGGAGAACAAAGATTTGCATCTATTGTTGCTAAAAGACTTGAGAGTTTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000139697-SBNO1:NM_001167856:20
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.217 A=NA C2=0.079
Domain overlap (PFAM):
C1:
PF138711=Helicase_C_4=FE(16.2=100)
A:
NA
C2:
PF138711=Helicase_C_4=FE(13.4=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
ATTGCTATCATCTCAGAAGCTGCC
R:
CAAACTCTCAAGTCTTTTAGCAACA
Band lengths:
246-1806
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)