MmuINT0138811 @ mm10
Intron Retention
Gene
ENSMUSG00000009614 | Sardh
Description
sarcosine dehydrogenase [Source:MGI Symbol;Acc:MGI:2183102]
Coordinates
chr2:27242702-27244523:-
Coord C1 exon
chr2:27244169-27244523
Coord A exon
chr2:27242881-27244168
Coord C2 exon
chr2:27242702-27242880
Length
1288 bp
Sequences
Splice sites
5' ss Seq
CAGGTGGGA
5' ss Score
6.71
3' ss Seq
TGTGTCCTTTTCTGGCCCAGGCT
3' ss Score
8.46
Exon sequences
Seq C1 exon
GTACAGGAGCCCTAAGTCCCCATGGCTTCACTGAGCCGGGTCCTACGTGTAGCTGCCACCTGTCCTCGAGGGAGAGCTGCTTGGAATCTGGGGCTACAACCCCTAGCCACAGAGGCCAGGCCCACCACCGAGAAGAGTGTTCCTTATCAGCGGACCCTGAAGGAGGAGGCCCAAGGTGCCTCCGTGGTGCCCCAAGGACCAAGCCAGCCCCTGCCTAGCACAGCCAATGTTGTGGTCATCGGTGGGGGCAGTTTGGGCTGCCAGACTCTGTATCACTTGGCTAAGCTGGGTGTAGGTGGAGCCGTGCTGCTGGAGAGAGAGCGACTGACCTCTGGGACCACCTGGCACACAGCAG
Seq A exon
GTGGGAACCTGGGTGCAGGCGGGTAGGTGGGACATAGTTGGGGGTGCAGGTGGGTAGGTGGGACATAGCTGGGGGTCAGTCTGGGTGAGGCAGTGGTGTTGGAGAGGAAAGATGTATAGTGGAGGTGGAAGGCCAGCCAGACTTCATTCTCTGAAGAGCTGTGCTAGGGAAAGTGGTAGGCACTACCTGTGGCCCTTTGGGTAGGGGTGAAGCTGCGTCCAGGCAGCTGTCTGAACTAAGAGTGGAACCCCTGTTCCCAGAGGAAGCCACTAGGCAGAGACACACCTGCTGGAGGACAGATGGCCCTGTGTGGTAGGGGCTCACATTCTGTGGCACTCTCCTGACTTACCCTGTGCATGCCCACTAAGCTCCCACAGTTCTATGTCTTCAACCCTTTAGCCAGTGGTGCCCTGGTGAACAGCTGCCAATCTGATGTGGTGTAAACATTTGCACCTTAGCGGCTGTCAAGAAGCCATCATGAGACTACTGCTGAACTTGGTAGCCTGGAGAACTGATAGTCTAGCCCGGAGCACACTGCCTCTAAGCCGGAAGTTCTCAACCTGTAGGTTGTGACCCCTTTTGGGGTTGCATATCATATATTGGTAGTATGATTAATAACAGTAGCAAAATTACAATTATAAAGTGTCAATGAAACAATTTTATGGCTGGGAGTCACCACAACATGAGGAACTGTATTGAAAAGTCTCAGTCTCGGCATTAGGAAGGTTGAGAACCTCTGCTTTAAACCCATCTCCCAAGGCCAGGCCGGCTGGGCTGTCAGGCCTTGGCCCTCCATGCTGCAGTAGCCTCATTGCTGGCCTCTATTCCTCAGCCTCTACTGTCTTAGCAAGACTGGGATTTCTGGGTCCAGTCAGTTTTCAGTCTCACCATTCACCTGCTCTGTGACTTTGAATTTGGTACCTATAAAGTTTACCTATGAAATAACCTCTCAAAGAGTGGTATGGTGGCCTAGACCTATCATGTCAGCACTTGGGAGCCAGAGATTGGAAGATGAAGAATTTAAGTTCATCGTTGGCCACATAGCAAGTTTGAGGCTAGCCTGGGCCTCTCAAGATTCTAGCTAGACTCTACCAGAGCTGGCACATAGGTGCTTGTTAATGGGAGCCCTAAATATTGTCACTAGGAGCTGTTCCAACATAGCCCTAACCTCCACCTGTGGCAGATTATGTCCTATCCTTCCTGGGTTCCCACTGTTCCTCATTATTTCTCTGGAAGAGGGCTGTGACACTACCCTGCAGGGGACTCACTGTGTCCTTTTCTGGCCCAG
Seq C2 exon
GCTTACTGTGGCAGCTGCGGCCCAGCGATGTGGAGGTAGAGCTTTTGGCTCACACACGGCAAGTGGTGAGCCGTGATCTGGAAGAGGAGACTGGGCTGCATACAGGCTGGATCCAGAATGGTGGCCTCTTCATCGCCTCTAACCAGCAACGCCTGAATGAATACAAGAGGCTCATGTCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000009614:ENSMUST00000102886:2
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.304 A=NA C2=0.017
Domain overlap (PFAM):
C1:
PF0126619=DAO=PU(11.9=38.4)
A:
NA
C2:
PF0126619=DAO=FE(16.4=100)
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:
TATCAGCGGACCCTGAAGGAG
R:
TTAGAGGCGATGAAGAGGCCA
Band lengths:
353-1641
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development
- Ribosome-engaged transcriptomes of neuronal types
- Neural differentiation time course
- Muscular differentiation time course
- Spermatogenesis cell types
- Reprogramming of fibroblasts to iPSCs
- Hematopoietic precursors and cell types