MmuINT0026560 @ mm9
Intron Retention
Gene
ENSMUSG00000042507 | C130039O16Rik
Description
RIKEN cDNA C130039O16 gene [Source:MGI Symbol;Acc:MGI:2685106]
Coordinates
chr12:85501429-85503551:-
Coord C1 exon
chr12:85503206-85503551
Coord A exon
chr12:85501496-85503205
Coord C2 exon
chr12:85501429-85501495
Length
1710 bp
Sequences
Splice sites
5' ss Seq
CTAGTAAGT
5' ss Score
8.78
3' ss Seq
AATTTGTTCTTTGCTCGTAGATA
3' ss Score
8.1
Exon sequences
Seq C1 exon
GCTGAAGACCTGAACGTCAAGTTGGAAGGGGAGCCTTCCATGCGGAAACCAAAGCAGCGGCCGCGGCCGGAGCCCCTCATCATCCCCACCAAGGCGGGCACTTTCATCGCCCCTCCTGTCTACTCCAACATCACCCCTTACCAGAGCCACCTGCGCTCTCCCGTGCGCCTTGCTGACCACCCCTCTGAGCGGAGCTTTGAGCCCCCCCCTTACACACCACCCCCCATTCTCAGCCCCGTCCGGGAAGGCTCTGGCCTCTACTTCAATGCCATCATATCAACCAGCAACATCCCGGCCCCTCCTCCTATCACGCCAAAGAGTGCCCATCGAACCCTGCTCCGCTCTA
Seq A exon
GTAAGTGACCCTGGTGGCTGTGGTGGCGGGTTATAGGGGACTGGGGGCTGGAGGACGACCTCTGCTATCTCCCCCTGGAGTGGAGTGGAGTGATGCTGGTTGGTCCTCCTGTTTGGATTCTCATCCTCTGTCCACCCTTTACTGTCAGACCTGCAAGTCCAACTGCTCAGACCCCAGTTCGTTCAATATTCAGCAAGGATCAGGATTTGATTAGTCATGCTTGGCTGCTGATACTCAGCTGATCCACAAACAGCAGTTCCTTACGATTCAATCTAATAGCTCCCTCCTCAGGCTGTGGTGGGGATCAGTTACATTAGCATTATTCATAGTAGGTGGCTGACCTGGTCTCCTGGGCTTGTTGATACGTTTTGGTCAAGAACAGGCCCTGGTGTTGTGAGGCTTAAAAATGTCCATTTTGCAAAGGGGTTCTTTCCTTTTGGAAAGTGGGATCACCTGACCCCTTACAGCAGACCGGCGCAGGTGCAGTCTTCTCCCAGTTAACCTCTGACCCCAGATACCACCCATGGTGTAGTTCTCTGGTGCCTCCTGGTGTCTGTGGATGGAAATTGCCTGGTGTTGGCAAGCACAGGTTTTGCTTACCTGGGAAGAAGTTTCTTTCTCTGGCTTGGTTTGGGTTGGAAATCACAGAGCAGAGCCAACAAGGTATCAGTCAGTGTGGCCAGCAAGTGTTTACTGAGCATTGTGTGTAAAACCTCACACTGGATCCTGTGCAGGCTCCAAGAATGTATGGGTACCATTATCTAGTCTAAAGAAAGTGCACGGTGGGATCATTGGGGAATTGACAAGAAAGCTTGGGAGACAGAAAAAGCAGAGGCTCCTAGCAGTGTGGGACCAGCAGGCAGTGAATGAGGCCGACACCAAGTTTCTAACCTGTGTGGCAGCCTCCTGGATAGATAAGGGAAGAATTTGGGAGAGGGTGGAGCCATAGCTGAGCTCGAACTGCAGAGTGGGAGGGGCAGGCACTGAAGGCGTGGAGTGGGGCTGAGCGGGGGAGTGAGGGCCGTGAGGTTGGGGTGAGAGCCTGGGTCATGGGGTGGGAGCACAGGGAACTGCCTGAAACAGCCGAGGGGGGGCAGACTTTGTCTCACTCACGTTGCAGGGGGCAGCAGCAGAGGTTTTGTGTGTTGTTTTGTTGTGATTAAGGGAGTGTTTTCATCCAGTCAGGCTTTAAGATTAACTTGGAGAAAGGTGAGGCCCCTCCCCCTCCCCCTCAAAAAAAAAAATCCAGAGAGAAGATGAAAAGATAATTATAAAGAGGCCTTTGACATCTCCCTGGTATGCTTCGTCCCGGCCTCTTTGATAGAACAAAACAAAAGTAAAACATAGCTCTATACTGCAGCGTGTGCAGAGAGAGCTCCTGGAAGCTGGGGCTGGGCTTCTGGGGGTTGTGCTGATAGCTGATAGTTGTGGAGTGCCAGGCTCTTTTTTAACTCACACATCTCATTACCTACAGGAGACAGAAAGAACGAACCCCTTTTGCAGATGTGAAAACTGAGGCACTCACATGTTTAATACGGGGCCGGAGTTGCACAGTCGTCAGATTGCAGAGCAAGGACAGAGGGTGCCTGGGTTCCGAGTGTACTCAATGAGTCACCGCTGTGACTCTTGCATGCAGGACAGCAGTCTAGGACAGGAGTGTTTTCCTGAAGGGAGGAAGAGGCCATTTACCAATTTGTTCTTTGCTCGTAG
Seq C2 exon
ATAGCTCTGAAGTCACCCCGCCTGTCCTCTCTGTGATGGGGGAGGCCACCCCTGTGAGCATCGAACC
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000042507-C130039O16Rik:NM_001163502:4
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.655 A=NA C2=0.261
Domain overlap (PFAM):
C1:
NO
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:
CAAGTTGGAAGGGGAGCCTTC
R:
GCGGGGTGACTTCAGAGCTAT
Band lengths:
350-2060
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: