HsaINT0145217 @ hg19
Intron Retention
Gene
ENSG00000139697 | SBNO1
Description
strawberry notch homolog 1 (Drosophila) [Source:HGNC Symbol;Acc:22973]
Coordinates
chr12:123808227-123810146:-
Coord C1 exon
chr12:123810049-123810146
Coord A exon
chr12:123808379-123810048
Coord C2 exon
chr12:123808227-123808378
Length
1670 bp
Sequences
Splice sites
5' ss Seq
CAAGTAATG
5' ss Score
2.09
3' ss Seq
TCACTGTTTCTCTCCTACAGAGG
3' ss Score
11.53
Exon sequences
Seq C1 exon
TGTGTTGTAATTGGTCTGCAGTCTACAGGAGAAGCTAGAACATTAGAAGCTTTGGAAGAGGGCGGGGGAGAATTGAATGATTTTGTTTCAACTGCCAA
Seq A exon
GTAATGTTTTTGTTCTTTTAATGTTTTTGTTTCTTTTTGAGTTCTTCCTTACCTTAGTTCCAATGTGGGCATTTCCTGGAGACAAAACTTTTGTTTCACCTGCATCATCTTTAAGTTTTCTTGATCTGAGTTTTCTGCTTTTCTGTAACAGTGTATCTATTGGAAAACAATAACAGAAATCTCATAATCCTAAAATGTTAAGCATTTTGCTAATATTACACAGAGTATGTGAACTAACAGAAGGGCTAGACTTTGTTTATCTTGTACATCTTGGAAATCTGTGACAGCTTGGCTTAGATTCAGTTTTAGTGTACTGTATTTGAAATTACCGTTATCCACAGGAACAGTAACTATAGTTTGTCCTAATATAACGAAGTCTACTTTATAAGTTGGCTGAGCATGGTGGCTCACAGCTGTAATCTCAGCACTTTGGGAGGCCAACATGGGCACATCACTTGAGGTCAGTAGTTTGAGACCAGCCTGGCCAAAATGGTGAAACCCCATCTCAACTAAAAATAAAAAAAATTAGTTGGGCATGGTGGCACACGTCCTGTAGTCCCACCTACCTGGGAGGCTGAGGCAGGAGAATCCATTGAACCCGTGAGGTGGAGGTTGCAGTGAGCCAAGATCGCACCACTCCACTCCACTCCCCTCTGGGCGGCAGAGTGAGACCCTGTCTCAAAAAAAAATAAAATAAAATAAAGTCTACTTTAAAAGTTGAAAATAAGCATGAGATCTTCAGAAATAGATTTTAAAATGTTTTAGGCATTGTTTTTAGTTTGCCTAACCTCCACATTCAAACTCTGGTAGTAAACTGAGCAAAATAAACTTGCTGCTCTACTATTTTGTGCCTCGGGATGCATTCAGATGCTCCTTTCAAAAGCAATACATGGGGCTCACGCCTGTAATCCAGGCACTTTGGGAGGCTGAGTCTGGTGGATCACGAGAGCTCAGGAGTTTGAGACCAGCCTGGCCAACACGGTGAAACCTCGTCTCTACTAAAAATACAAAAACTAGCCAGGCGTGGTGGCGGGCACCTGTAATCCCAGCTACTGGAGAGGCTGAGGCAGGAGAATTGCTTGAACCCAGGCGGCGGAGGTTGCAGTGAGCTGAGATGGCACCATTGCACTCCAGCCTGGGTGACAGAGAGACTCGGTCTCAAAAAAAAAAAAAAAAAGAAAAAAGCAAGACATACACCTGCTAATCTATATTTTTCTGTACATAATTGCCTAGAACTACCGTGTCCAGAATGGCAGCCGCTTGTCACATGTGGCTATTGAGCAGTTGAAATGACTGGTCCATATTGAGATGTTATTATATGTGTACTGAGCCAGGTTTCAAAGACTCCTTAAGAGAAAATAACATAAAACATATGTGTTGACATGGTATATTGAGTTAAAATGTATTATTAAAATTAGTTCCACCAGTTTTATTTATTTTTTACTTTTTTAATTTAAGCTACCAGAAAATACAATAATTGTGTATGTGGTTTGGCTTGCATTCTTATTATTTAGTTGGACAGCTTTGGGCTAGAAAATTAAAATTTATTTGAGCTCGTTTATCAGTATTTTGTAAAACTGAACAAAGTATATTTCAATATATTTAATAATACTTTACATATAATTATTTTGTCAACTGAAGCAGTAATTGTCACTGTTTCTCTCCTACAG
Seq C2 exon
AGGTGTGTTGCAGTCACTCATTGAAAAACATTTTCCTGCTCCAGACAGGAAAAAACTTTATAGTTTACTAGGAATCGATTTGACAGCTCCAAGTAACAACAGTTCGCCAAGAGATAGTCCTTGTAAAGAAAATAAAATAAAGAAGCGGAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000139697-SBNO1:NM_001167856:14
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.030 A=NA C2=0.412
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
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:
TGTGTTGTAATTGGTCTGCAGTCT
R:
TTTTCTTTACAAGGACTATCTCTTGG
Band lengths:
230-1900
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)