MmuINT0149670 @ mm9
Intron Retention
Gene
ENSMUSG00000047793 | Sned1
Description
sushi, nidogen and EGF-like domains 1 [Source:MGI Symbol;Acc:MGI:3045960]
Coordinates
chr1:95156222-95158351:+
Coord C1 exon
chr1:95156222-95156384
Coord A exon
chr1:95156385-95158225
Coord C2 exon
chr1:95158226-95158351
Length
1841 bp
Sequences
Splice sites
5' ss Seq
CAAGTAAGA
5' ss Score
7.61
3' ss Seq
GCTCCTTCCTGTGTCCACAGCCT
3' ss Score
9.47
Exon sequences
Seq C1 exon
GCAGGTTTCAACGCAGGTGATGGGCACCGCTACTTCAACATCCCCGGGTCGCGCACAGCAGACATGGCTGAGGTGGAGACCACCACCAACGTGGGCGTGCCCGGCCGCTGGGCGTTTAGAATCGATGATGCCCAGGTGCGCGTGGGGGGCTGCGGCCATACAA
Seq A exon
GTAAGAGGCTCAGGGAGGGGAGGGTTGAGGAACCCTGTGGCAGTAGGGGTGGGGCAGAGGGGTTAGAACCTATACCCCACCTCACTAAATCCCCACACACACCCCTGCCCCACAGCCCATCCCGTCCCATACCTCAAGTGACCTGGGTGTTCTGGAGAGAGGAACAAAGCAGGGTTGCCACATCCCACCCCTGCCTCCATCTGGGGTGGGGGTTGAGGGGACAGGGACATCCATAGCCCTGATGTTGGTGACAAGCCAGAGCATTTTATAGTCCTGGTGGTCTAGTAGCACAAGCAGGTAGATGACCCCAGTAGCCCACACTAGTCGTGTGCCCACTCAGGAACCCTAGCTCTACTGTCATGGCTCCTCTAGAAGGTACCACACCCTGAAGCACCCTGCCCACAATGCAGAGATGCCAGGCATTGGCTGGCTGACCTGCCAATTAGGAGATCCCCTCATCACAAACCCTCCTAAACCTGCATTAAAGACAGGCTGCTGCTGGGACCCACCCTACAAACGTGTTGCTCATGTGAATGAGGCCACAGAACAGGGTGCCTTTCCCCAGCACTGAATCCCCTAAAGAGAACTCAGCTGGGAGAGCACACAGAGCCACTGAGAGTCAGGGAGACTGTCTGGTGAAGGGGAGATGAGGGTGTGTAGTACTGGGGAGGGAGAATCTGGAACACACCCCGGCATGCTGGGTACTGAGATCCACCTGACTGCACATAGCAGGCCAGCCTGGGAAGCCAAAGCGGAACTCAGTGCCATCCCAGCCCCAGAGCAACAAGGGTAGAATCCCAGGGTAGCCCCAACCCCTCTCCTGGCCAGCAATCAGCTCTGACATCAGGACTCTGGGCCATAGCATCTGAAGTGGTCCTGCAGGCGCTGCTTGTGGTGTGGGCTGGGGGGGGGGGTGTCCCTTTCAAAGGCCAGAGTGTTAGGTTCTGATGAGAATCAAGGTACAATTGTAGGCAAACCTTGCTTTTCAAGCTACATCAGCTCAGGTGGAAGGGGACTCTCAGAAGAGAGGATGAAGTGCCATCCCATTACGGAGCACCTTTTCCCAGGCTTCTGAGATAAGAAGGCACAGGAAACAGCTGCAGGGATGCCTTGGTGCCTGTGGTCCCTGGGAGCCAGGGACACAGCTAAACTGCAAGCCAAGGCCAGTTATGGGGCATTACATAGACACAAGCTTGCTGAGAAGCAGCCAGTGCCTGTGTCTGGAAGTGTAACTCCTAAGCAAGCCCGGCTCCTCTTGCAGCCATGGCTACAACAGAGCAACCAAATTTCAAGTAGGCCAGGTGAGCACAGTGCTGCTAAGTGAGGCCAGCTGACGGAATGGTAAGCTCCCTGTCCTGAAGGCACCCACAGTCTGAATGGTGTGCTGGATCACTGGGCCTCTCTGGAATCTCCCTGCAGCTCGGGGAGCCATGATAACCACTGGCTGTAATAACTAAGTGCCAGTTTAGGAAACCAGGAGGGTGGCTGAACAGCCCTGAGCTTCTACAAGTGTCCATGGTAGAGGTGGAAAAGATTAAAGAGATAAAAGGAGGAGCTATGGGTATAGGTGGTTGTGGGGGTGTCTGCCTTCACAGGAAGCCTAAGTCAGAACTTAGGGCATTAACAAACAGCAAAAGATCCTGACAAGAGTATCTGCCAGGCAAACTGGGCTCCAACTCAAAGACCCAGAACGTGAGCACGAAGATGCACCGTCACCAATGTCTTGGTCGCTAAGCTGACCTTTTGATGGAGAGAAGGGAGATGCAGCCATTGCAGGTGGCTCTCTTGCCCACCTCCTAGATTCAGTGGCATGAGGCTTGGGCTCCTTCCTGTGTCCACAG
Seq C2 exon
CCTCTGTGTGCCTGGTCCTGCGTCCATGCCTCAATGGTGGCAAGTGCATTGATGACTGCGTCACGGGCAATCCCTCTTACACCTGTTCCTGTCTCGCTGGCTTCACAGGCCGGAGATGCCACCTGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000047793-Sned1:NM_172463:4
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.055 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF061199=NIDO=PD(47.3=78.2)
A:
NA
C2:
PF0000822=EGF=WD(100=83.7)
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:
AGGTTTCAACGCAGGTGATGG
R:
CCAGGTGGCATCTCCGGC
Band lengths:
287-2128
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: