MmuINT0139097 @ mm9
Intron Retention
Gene
ENSMUSG00000038095 | Sbno1
Description
sno, strawberry notch homolog 1 (Drosophila) [Source:MGI Symbol;Acc:MGI:2384298]
Coordinates
chr5:124858486-124860391:-
Coord C1 exon
chr5:124860079-124860391
Coord A exon
chr5:124858587-124860078
Coord C2 exon
chr5:124858486-124858586
Length
1492 bp
Sequences
Splice sites
5' ss Seq
CTAGTAAGT
5' ss Score
8.78
3' ss Seq
ACCCCCTTTTCTTCCTGCAGCTG
3' ss Score
12.37
Exon sequences
Seq C1 exon
CAGCAGCCTCCATCCACTACAACGTTTGTGCTGAATCAAATAAATCAACTTCCAACTTTGGGATCTACAATTGTAATGACTAAAACACCACCTGCAACAACGAATAGGCAAACCATCACTTTGACAAAGTTCATCCAGACCACTGCAAACACACGCCCTTCAGTTTCAGCACCAGCAGTACGAAATGCCATGCCCGCTGCTCCTTCAAAAGACCAGGTTCAGCTAAAGGATTTACTCAAAAATAATAGTTTAAACGAACTCATGAAACTGAAGCCACCCGCCAATATTGCTCAGCCAGTTGCAACTGCAGCTA
Seq A exon
GTAAGTCCATTTTCAGCCATTTGAACTTTGTCTTTCCCTAGCAGTTTTGTTTGTGTGTGTGTTTTTTTTTTAATTTAATTTTTTTAAGACTTATTTATTTATTATCATATGTAAGTACACTGTAGCTGTCTTCAGACATACAGACATACCAGAAGAGGGAGTCAGGTCTCTTTACGGATGGTTGTGAGCCACCACGTGGTTGCTGGGATTTGAACTCGGGACCTTTGTAAGAGCAGTCAGAGCTCTTAACCACTGAGCCATTTCTCCAGCCCCGTGTGTGTGAGTTTTACAAGTAGTTTTGGATGTTGTGTTTAATATTTATTTATTCTTTGTTTGTGTGGGCCTGAGTGTGTTTATATGTACATATGGATGAAGCACCTGTGGAGGCCAGAAGAACTGTCAGAGTCCACTGGAACCGGAGTTAGATTTTTTTTTTTTAACACTTAATTTCTTTTTCTTTTGCTTTTGTTTGTTTGTTTGTGAGAATGGTTTTTCTGTGTGACCCTGGTTGTCCTGGAACTTTGTAGACCAGAAATCTGCCTGCCTCTGCCTCCCAAGTGCTGGGATTAAAGGCGTGTGCCACCACTGCCCAGCCTGGCTAATGTATCTTACTTGTGGAACTTTTTTCACAATTTAAAAATTTCTCATGTACATTTTTTCCCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTCCCTCTCTCTCTCTCTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTCCTTTCTTGTTTGTTTGTTTGTTTGTTTGTTTGTTTTTTTGGTTTTTTTCAAGACAGTGTTTCTCTGTATAGCCCTGGCTGTCCTGGAACTTACTATGTAGACCAGGCTGGCCTCAAACTGAGAAATCCACCTGCCTCTGCCTCCCAAGTGCTGGAATTAAAGGCGTGCCCCACCACGCCCGGCTCCCTTTCTTTTTTTTGTGACTGGGTTTCACTATATAGCCAGGTTTACCTGGAGATACCTATGTGAACCAGGATGGCCTCAGATCACAAATCTACCTGCCATGGCTTTTTGAATGCTGGGATTAAAAGCATTTTCCATCCAGACAGACCCACATTCCCCTTTCAGTTACTGGTTTACTTAAGCGTTCTATAAAACCATACAGGTTTGAGGTTCAGTGATTATATCATTCCACTTGGGTTTGATTCTCAGCACCTACATCATGTAGGACACAATCACCGTAACTACTTCCAAGAGGATCTTATGTCCAATTTTAGCTTCTGTAGGCACTGCACACAAATGGTATAGAATATATATAAATATAAATATACATAAAATACTAAGTAAATCTTCAAAATTACCTACAGTAATTTGAATGCTTTCATGGTTATACTTAATTTAGTGGTACAATTTTTTGACACTCTTTTTTTTTTTTTAAATGGATAAAGTGCTGAATTTTTAAATTAGAGGAAAGGAAATTGAGATGTGTAACTTGTAACCCCCTTTTCTTCCTGCAG
Seq C2 exon
CTGATGTCAGTAATGGTGCAGTTAAGAAGGAGTCTTCTAATAAAGAAGTGGCGAGGATATGGATAAATGACATGAAGATGAGGAGCTTTTCCCCCACCATG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000038095-Sbno1:NM_001081203:4
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.894 A=NA C2=0.382
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:
GCAGCCTCCATCCACTACAAC
R:
AGACTCCTTCTTAACTGCACCA
Band lengths:
346-1838
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development
- Muscular differentiation time course
- Spermatogenesis cell types
- Reprogramming of fibroblasts to iPSCs
- Hematopoietic precursors and cell types
Other AS DBs: