MmuINT0005176 @ mm9
Intron Retention
Gene
ENSMUSG00000040412 | 5330417C22Rik
Description
RIKEN cDNA 5330417C22 gene [Source:MGI Symbol;Acc:MGI:1923930]
Coordinates
chr3:108270671-108272583:-
Coord C1 exon
chr3:108272446-108272583
Coord A exon
chr3:108270935-108272445
Coord C2 exon
chr3:108270671-108270934
Length
1511 bp
Sequences
Splice sites
5' ss Seq
ACAGTGAGT
5' ss Score
8.34
3' ss Seq
TTTTGTTCCCTCATCTCCAGGGC
3' ss Score
10.74
Exon sequences
Seq C1 exon
GGCATGAATTCCAGGACCAATACTCCTGTGGAGACGTGGAAGGGCACCAAAGGCAAGCAGTCCTATACCTACACCATCGAAGAGAATGCTACTGTGAGCTTCACATGGGCCTTCCAGAGGACCACCCTTCATGAAACA
Seq A exon
GTGAGTCCCTCCCCTCCCTCCCGTCCCTCCCGTCCCTCCCATCCCTCCCTTCCCTCCCCTCCCTCCCGTCCCTCCTGTCCCTCCTGTCCCTCCTGTCCCTGGTGCAGACTGTGACCACAGGGCTCCTGCTGTGAGCTCATGCTGGCTTCTGAGTTCATAATCTGCAGGAGCCAAGCAGGAATGCTAAGCATGGCCTCTGAGGGCTTGAGCCTTTTCTAAATGACTTCCCCTTACAGTCTCTACCACAAGTGAAGCCAGACATATAGCTATTTTTAAAAATAATCACTCTGTTTTTCTTTCATTTTTGAGACAGGGTCTTGGTCTGTAACCCAGGCTGACCTAGAACCTGTAATCCTCATGCCTTAGCTTTCCCAGAGCTAAGATGAAAAGCTTTGCTTTATTTTCTTAACTCAAAAAACAAAAAAAAAACAAAAAAAAAAAAACAAAACCAAACAGATGTACTGCAGAAAACAAATCAACCTGGGCTGTAAAGTGGGCCCTGTCTCAACAAACAAACAAACAAAAAACCAAATCACCCATAAACCTGTTACCCAGAGATAACCCAATTACTATCTTGGAGAGTGTGCATTCTTTGTTTCTATGTCTATCTCTGCCCCTCTCTGCATCCCTTATGTATACTAAGTCTATATTTTCATCCCCACTCCTCAGTCCCTGGCTTTTAGAGACAGGCCATTCTAATCCAGGCTGGTTGTCTTCCACCTTGCGATCCTCCTGCCTCTGCCCCTGAGTGCTGGGATTCTAGGGTAGTAAGACCACACCCAGTCCTAATTTTGATTTCTTTTTAAGTACGTGGATTTTTTTTCTTTTTTCTTTGACAAAGACCCCCCCCCATATATTAGAATTTCCTATAAATTCCCCATGGCGCATAACATGGAACTTAAAATGGGTTAGTCTTGTTAATTACACAAAATATACCTTAAAAGCCATTGTTCTTTTTAAAGTTAAACTATTTATTTATTTACTTACTTACTTATTTACTTAACTTTTGGTTTTTTGAGACAGGGTTTCTCTGTGTAGAGCTCCACCTGCCTCTGCCTCCCAAGGGCTGGGATTAAAGGTGCACACCACCACCACCTAGCTCTCTATTTTTAGTATCGTTCATCTTTAATTTTCATACAAAGAGCCACCATGAAATAAAGTGAGAAAGATGCTTCTAGTGGTTCAGTCAGTACCAGCTGTTGCCATGGAGCCCGAGGACCTGGGTTTGATCTCTAGCATCCATGTAAAAGCCAGGACATGAGACAATTAGTTCAGTGAGAGACCCTGTCTCAAAAAATGAGATGGAGAGTGATGAAAGGAACGTCTGATATCCACATCTGGCTTCTACATGCATACTTACATATGTGCATGTACATTCACATACACATATACACATGTACACACGTACACACGTGTACATGCACAAGTAAAGTGAAAATAAACTCTGCTCTTCCTATGGCTGCTGCTGCTTCAGGCCTCTCCTTTCTCTGCTTTTGTTCCCTCATCTCCAG
Seq C2 exon
GGCAGGAAGTATACTAATGATGTCGCCAAGATCTACTCAATCAATGTCACCAACGTCATGGGGGGCGTGGCCTCCTACTGCCGTCCCTGTGCCCTAGAAGCCTCTGATTTGGGCTCCTCCTGCACCTCTTGTCCTGCTGGCCATTACATCAACCGGGATTCTGGGACCTGCCACCTCTGTCCCTCTAACACCATCCTGAAAGCTCACCAGCCTTACGGTGCACAGGCCTGTGTGCCCTGTGGTCCAGGGACCAAGAATAACAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000040412-5330417C22Rik:NM_001033304:12
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
No protein impact description available
No structure available
Features
Disorder rate (Iupred):
C1=0.065 A=NA C2=0.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF076998=GCC2_GCC3=WD(100=45.5),PF075629=NCD3G=WD(100=30.7),PF076998=GCC2_GCC3=PU(80.4=46.6)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Rat
(rn6)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CAGGACCAATACTCCTGTGGA
R:
CGTAAGGCTGGTGAGCTTTCA
Band lengths:
344-1855
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Muscular differentiation time course
- Spermatogenesis cell types
- Reprogramming of fibroblasts to iPSCs
- Hematopoietic precursors and cell types
Other AS DBs: