MmuINT0005185 @ mm10
Intron Retention
Gene
ENSMUSG00000040412 | 5330417C22Rik
Description
RIKEN cDNA 5330417C22 gene [Source:MGI Symbol;Acc:MGI:1923930]
Coordinates
chr3:108455694-108459850:-
Coord C1 exon
chr3:108459685-108459850
Coord A exon
chr3:108458469-108459684
Coord C2 exon
chr3:108455694-108458468
Length
1216 bp
Sequences
Splice sites
5' ss Seq
AAGGTAGAG
5' ss Score
6.38
3' ss Seq
TGTCACCATCTCTCTTTCAGAGG
3' ss Score
10.68
Exon sequences
Seq C1 exon
ATTAGAATACAAATACTCCAAGTTGGTAATGAACGCTACTCTTAAAGACTGCGACCTGCCGGCAGCAGACAGCTGTGCCATCATGGAAGGAGAGGACGTGGAGGATGACTTCATCTTTACCAGCAAGAAGTCCCTCTTTGGGAAGATCAAATCCTTTACCTCCAAG
Seq A exon
GTAGAGAGGGATGAGAACTCAGCTTGGGGAGGTCAGGGGGTGGAGCGTGGACACTGGGATACTGAGTGGCCCTGCTCCGTACAAGACCTGTACTCTGATCCCCACTCCCAGAACTCTCCTGCCTCTCCTAAAAGTGTCTCCTTCCCTCTGCAGCTCTCAACAATAACTCTCTTCCCTGGAGCCTAGCCAGTTCTTGACCAGGCTCCTTCCTGCCAGTGTGTATTCTGGTGGGTGGGTTGTTAGGGTCTTTTAACTTCCAGATGGAGTATTGAACCATTTGTGTGTAATGGTTACACACACACACACACACACACACACACACACACACACACGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGGAGAGAGAATTTCCTTTTCTTTATTTTCCTTGAGTGAAGAGGAAGCCATCTCTAGGTTTGATTCCTGTTAGAAGCCAGGGCCTCAGAGCCTTTAGCCAGTGGAGGGTGCTATCCCCAAGGTGTGTGTGTGCCCCATCCTGAGTGGCTGAGTCATAGCCAAGCGTAAACTGTGGCTGCTATGTAATTCTGAACTGGGCGGGCTGGCTAGGTGGTGCGGGTGTGTAGGTGCGTATGAAGCTCATAAAGGCAATACAGACACCACTGTCTCTGGGCGTAGGGCCAGCAGAGGGCATCCGAACAGCTTCCTCGAGCCGAGCACACACCTGACTACCCTGGCGCACAAGGGAGTATTTCAAACAGGTGTGAATGAGGAGGGCACCAGCGGCTAGGAGGGGGCAGGAAGCCTGCTGAAGAAGAGTTGGCAGTCTGTCCAGTCCCTGGGTCTTGTTTCCTTTGTGCTGACTTGTCAGGGTGACTCCCTTGGCCAACGTGGGCCTTGATTTTTTTTTTTTTCTTTTTTCTCCCACCAGTGAGAGATAGTTAACCCTGGGGACCTCTTAGGGCTGTCTGGAACTTCTAGAACTCAGCAAGGATGCAAAGCAGCAATCATAAGGCTCTCACGCTCTGACTGAGTCTGCGGAGAGCAGGGAGGGGCAGAGGATTACTCGTTCCTGTGTCGTCGTCGTCCCGTCCCCCCACCCCCAAAGCCACCGGAAGCAGGAAGTCCAGAAGGGTTCCTCTGTCACCTATTTTTCCATTTCTCTTCTTTGTCCCCTTAATGTGTCCCCGTGCAGCAGGCAGCTCCTGTCACCATCTCTCTTTCAG
Seq C2 exon
AGGACTCCTGATGGATTTGACTCGGTGCCGCTGAAGACGTCTTCAGGAGGCCCAGACATGGACATGTGAGAGGTGCCCGTCCTGCCTCGCCTGCCTCCTCACCTGGGCACACTACCCTGCAGGCCTGTGGCAGTTTAGGTGCCAGCAACCCTGCGCTCCCCGCTGCTGGGAATCTCTTCATTGTGGCCTTATCAGAAGTTTGGATTTCAGACCCTTGTTTTTTATAGAGTACCCAAACCTGTCTCTACGCTTGCCTCAAGCCTACCAAATATACCCACACTTCGTGTACTGTTTCCTTGCTTACATCTTGTTTTCTAAACACAGTCCACCCATGGGAGACTCATCTACCCAGAATTCTTAGCGGTTTTCAGTAAAAGTAGTTTGTTTTTTGTTTTTTTTTAAATAAGTACGAAATTGGCTTCTAGCCTCCTGTGTGAGGGCGGGGGCAGCTGGGAGGTTTTCTGGTCAGATACAGGCTTTCAGCTCATGATGTCTTTAGAAGGGGGCTGTGGTCTGAGGGACAGTCCTCATGGCAGCCTCGACTTATTTCTCCTGGGTAATAAGTTGGAGCAGAGAGCAGTGGACAGTCTGAAGGCATGGTGGGTGAAGCCTGTGTAAGAAAACACACACACACACACACACACAAAACTCAAAAAAAGGCAAAGTGTCTGTGTGTGTGTGGGGGGGGGGGGGTGTTTGTTTTGTTTTATAACCAGGAACCTCATTTCCTTCTCTTTTAATGATAAATATTCTCATTAAAGGCAAAGGAAGTTATTTACCAAGAACTTGCCCAAAGTCCAATAGATCTATCCTCCACGACTGTTTTTGTCAAATATCCCTCCCATTTCCTTATGACACTAGAAAGAACCAGGTAAGTCTAGCTATACCTTCCATTGGCTTTGCTGGAAGGGAATAAACGCTTGCCAGTGAGAAACACCCCCATCTGTGAGGACCTCAGTCCTAGAGGCCTAGAGTATCATGGGATGGAGCATCTTATTTAGAAAGAACACAGGGGGCCAAAGGTTTGATGGGGCAGTATTAGACTCCAGCCCACTGTGGCATGGACCAGCTATGGTCATATCTGTTTCTGTCTTTAACTTGCTAGGCCAACAAAGTTAAAAACTTGCAGACTGACCAGAAAGGAGCTGAACGTCAGGCAGGTACAAACCAATCTTCAGGGAGAAAAAGTAGGGATGTCTTACAAGGCCTACACCCAACTGGGGCATTTGTCACTCCTAAGCCTCTGTCCTGGCTCTGGCCTATTCTCATTTCACTTGTGCATAAATATCTAAAAGACTCCTGGCCCTCATTCTGGCAACACCCCTCTGAAAAGTAGATTAGGTACCAACTCGCAAGTAGAGTGGGATTCCTCTTCCCATCTCCCTTTCACTCCAGCTATAATCAGTAGAAAACCTAGAATAGAATAATACAGAGAATAATTTCCAGTTAACTTTCCTCCCTACTACTGGGAATTGAACCTCTTTCATTCCATACCGGAATAGCCATCTCTTGGTCAAGCCTGAGTTGCCCATGGTCTTCACCTGTGCCTTTCCCCCAGTGACAGGTGGTTGGTATAAGACAGAGAGGCATTTCTGAGGTGTTTGTCAGCCACAAAATGGCTTGCCCATCTGACTAGCCATGGCTGCTCTCATGATGGCTTCTAAGAATCAGAAAGAAGTGAAGCTACGCCATGACTTTTGGCCATCAAAGGCATCAGTGATAGCTAGACAAACCTAGAAGCTTTTCTTTGGGAGTTCAAGTTGTCCCTCATTTTGTGGCTCTCAGCACTTTGATCATACGGGAATATTCTTGAGTGGCTATGTACACCCAGGCCATGAGCTCACAGCCAGTCTCCTGCAGCCTCTTAGATGTCTGCTTCCCATGGAATAACTGCTTTCTGTGTTGAAGATCACAGGAGATATTTAGACTGTTCTGGAAGACATGGGGGAAAGTCTATCTCTTTGGACTTCTTTATTCAGACATCCTGGAATTGAATGTCCTTCCTCCCAAGCATCCTCAAACAGCACTGATTCAATGATAGCACTTTTTGCACCTCTACCTTACTCTTTCCTGGGATGGTTTCCAAAGGAAGAGGCTCACCTGTTGCTTCTCTGGCAGCTCAACAAGTTCAGATAATTTCAGGGGCTCTACTAACACATAATTCACATACTGCATAAGTCACCCTTTCAAAGCATACAACTTTGTGACTTTAGGTATATCAATTTTAGTTTTCTGGGCTGAAGATGAAACCCAGGGTGTCTCACATGTTAAGCAAAGTGTTCTACCACTGAGCTACATCATTGACCATGAACATACAGTTGAGAACACATACACTAGGTCTGCAAGGGAGAACGGCTTTAGTCTTTGAGCCAGGACTGTGGTAGTCTGCGCAAACTTTAGGGCCAGAGAGTTGGCTCAGGAGATAATGTCTAATCTCTATTTGGATATATAGAGTCCTAGAATACATAATTTCATCCTGTAGTTAGTCATCACCTGTATTTGGCTGGGAATACATATGAAGATTATGGTATATCCAAGGCCCAGGGGATTTCTTATGCCATCAAAACTTTTTTTTTTTTTGGTCCAACTATATTAAAGACTGACTATATTTATATAACAGAAGCTTTGTAAAAGATTTTTTGGCTTTGTGAAATCATATCTGTGTCTCATCAAGACATGTTGGATTCCCTTTTTATTCTGTATTTCAAGCATTTAGTTTATTAGGGATGGGTATGCATGTCTCCCCCTCCCCCAAAATAAAAACATATCTTTTGA
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000040412:ENSMUST00000106625:21
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.182
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:
ACAGCTGTGCCATCATGGAAG
R:
AGCGTAGAGACAGGTTTGGGT
Band lengths:
349-1565
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