MmuINT0026555 @ mm9
Intron Retention
Gene
ENSMUSG00000042507 | C130039O16Rik
Description
RIKEN cDNA C130039O16 gene [Source:MGI Symbol;Acc:MGI:2685106]
Coordinates
chr12:85495845-85497526:-
Coord C1 exon
chr12:85497377-85497526
Coord A exon
chr12:85496058-85497376
Coord C2 exon
chr12:85495845-85496057
Length
1319 bp
Sequences
Splice sites
5' ss Seq
AAGGTGAGT
5' ss Score
10.47
3' ss Seq
TTCATTCTTGTCCCCCATAGACT
3' ss Score
9.8
Exon sequences
Seq C1 exon
ATCCAGACCAAGACTGTGGCCCAGTGCGTGGAATTCTACTACACCTACAAGAAACAGGTGAAAATCGGCCGCAACGGGACGCTCACCTTCGGCGACCTGGATATCGGTGACGAGAAGTCAGGCCAAGAGGAGGTTGAGGTGGACGTTAAG
Seq A exon
GTGAGTCCTTCCCCGGCTCTGCTGCATCACTCTGGGTAACACCTTAGGCCAGGACCTAACTGGAGGCCTGAGGACTCTCCTGGGGTTTATACAGGGCTGACAGAGGAGGAGAGCAGGTCCCTGGCAGCTCCCGGGAGCTGGTGCCCCAGGCCCTGGCCCTTTTGAGCTCTCTCCGGTATCGACTGTCGCGGTCGCAGTGATGGTGCTGATGCTGAACACTGGAGAGTCGGCGGCACAGCTTTGGCTTACTGCCTCTTCTGAGCAGACCACCAAGGTCACTTCTGGGCTCCAGCTCTTCTTGTACCACCTTTATGATTTCTGCTTTGTCTGTGCGTTAACACACACCACAATTACTGTTTCTGTCACGTCTCACACAACTTTTTTTTTAAAAGATTTATTTATTTATTTATTTTATGTATTCATATATCTGTACACTGTAGCTGTACAGATGGTTGTGAGCCACCATGTGGTTGCTGAGATTTGAACTTAGGACCTTCAGAAGAGCAGTCAGTGCTCTTAACCGCTGAGCCATCTCTCCAGCCCCCCACACAACTTTTATTATTAATTTTTTTTTTGAGTCAGCCCACTCTTTTTCTCAAAAGGGAAGCTTTATATTACAATCATAAATAGAAACCAGTATTGTTGCCTATAAATAGAAGGTACTGGGAAAAATAAGTCCACATGAAAACCAAACCCTGTCACTAAATGCCAGCTACACGCTGCAGTTGCTTGCCAGGCCTCTGAGACAGGGCTGGCTTCTCATTTAGGCAGATTATCAAGTCTAGGGAAGAGGCACATTAACACCAACCCTGACGTGGTCTTTGAGAGACACTGTGATTTAATTTTGTGCCCAGAAATCCTCTTGACCTTGTCTCTAGGTTACAAGGCAAGATTTGGTGGTGTTCTGCTTTGAGATGAGGGAGTATTTTGGTCCCCATATTATAGATGGGGAATGGAGATAAAGTATCACAGACAGTTAAATTGGAGCTCAGAGCTACTGCCTGGCACACGAGGTCACTGTGTCCAAAGGGTGCTCAAAAGATTCTGGGCATCTCTCCAGGAGGCCAGGTGGTTTGTGGATCCTGGCAAGTTCCCTCCATATCCCTGGCTCAGTCTCACCCAGAGGGCACCCAGGGTCAAGACTATCATCCTCTTTCCGGGCCAACTGGCCATAGGGAAGCTGTGACTTATGACAGAGTCTCAGTACAAGAGGCTGGACTGGGCCAAGACAGGACTGCAGACCCCGCAGGTGCTTCAGAGCCTTGGGTGGATCAGAGTCTGCACTCTGGAATGACTGGGTTCATTCTTGTCCCCCATAG
Seq C2 exon
ACTTCTCAGAAGTTCCCAAGGGTGCCTCCTCCCAGAAGAGAGTCCCCAAGTGAAGAGAGGCTGGAGCCTAAGAGAGAAGTGACAGAACCCAGGAAGGAGGGGGAGGAGGAGGTGCCAGACACCCAGGAGAAGGGAGAGCAGGAGGAGGGGCGTGAGCGCTGCCGGCGGGCCGCTGCCGTCAAAGCTACACAGACACTACAGGCCAATGAGGCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000042507-C130039O16Rik:NM_001163502:10
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.300 A=NA C2=1.000
Domain overlap (PFAM):
C1:
PF0024926=Myb_DNA-binding=PD(34.8=32.0)
A:
NA
C2:
NO
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:
ATCCAGACCAAGACTGTGGCC
R:
GTCTGTGTAGCTTTGACGGCA
Band lengths:
344-1663
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: