MmuINT0005397 @ mm9
Intron Retention
Gene
ENSMUSG00000024269 | 5730494M16Rik
Description
RIKEN cDNA 5730494M16 gene [Source:MGI Symbol;Acc:MGI:1913898]
Coordinates
chr18:25298947-25300138:-
Coord C1 exon
chr18:25300022-25300138
Coord A exon
chr18:25299108-25300021
Coord C2 exon
chr18:25298947-25299107
Length
914 bp
Sequences
Splice sites
5' ss Seq
CTGGTAAAG
5' ss Score
5.75
3' ss Seq
AACTTCTTGTGCTGTTTTAGGGT
3' ss Score
10
Exon sequences
Seq C1 exon
GAAATGAAGACCACCAGCTAGAGAAGCCTCACTTTGACTGTCGCAGTGCAATATTTGAGCTGGATTCATGCAATGGGAATGGGAAAGTTTGCCTCGTCTACAAAAATGGGAAACCTG
Seq A exon
GTAAAGATCATTTCCAAAGTATGATCCTACAGTATAGATGTGTTCTTCCTGAGCTTGCCTGTCAGCCGTCACTGAATGAAAAGCTCCCCGAGACACACTCAGCCTCAGAACAATTAATAGGATGGCAACATACAAATGAGAATGGGCTGGTAGTTTTGGAAAGGAAGAGAATGGGGAAAATGTTAGAGTTATCTAGAAAGCTGATGATCCACAATGGGCTACAGGTAATTCATAAACAGGCTTAAGATAGGAACTGGCCTAATAGTGCCTGGGTCAGCTGACCTAGGATAGCCTATCAAGGAGCAGGATTGTAGGGGTGAGGTGATATACGCCTGTGGGTTGAATAACCCATTCACTGGGGTCACCTAAGAACATCAGAAAACACAAATATTTATATTACTATTCATAACAGTAGCAGAATTAGTTAAGAAGTAGCAACAAAAATAATTTTATGGCTGGAGGTCACCACAACCTGAGGAACTGTAAAGGGTTGTGGCAGTAGGAAGGTTGAGAGCCACTGGTATAGACTCTTTTACCTTGGTTTTTGGTTTGGTTTTGTTTTCCATAGCACTTTTTATTAAGAGACCTCTTTTTAAAAGACTGATCCATTCAAGGTTTCTTTCCATCAAAAAAGAAGACGGAGTGCTCAGTCCGCAGAGAACAGAAGAATCTGCTAAGATAGCCTTAATGAGCTGCCACAGGGCCAAAGCAAGCAGGTATATCCACGGGCTGATCTCTGAGTATCAAATAAACAGGTAGGAGCAGCTAGAACAGAGCAGGACTAGAAGCCTAAGAGGGAAGTGTTATGTTTTCAACCCTCTCTACTATGAAGTTTCTCTTAACTATCAATGTATATTGACATTGTATTTAAAAGGGAAAATGCATTAACTGTCTAACTTCTTGTGCTGTTTTAG
Seq C2 exon
GGTTAGCTCATGACACTGAGATATGGTTCCTGGACAGAGCATTATACTGGCACTTTCTCACGGATACCTTTACCGCCTATTACCGCCTGCTCATCACCCACCTGGGCCTGCCCCAGTGGCAGTATGCCTTTACCAGCTATGGCATTAGCCCACAGGCCAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000024269-5730494M16Rik:NM_001142698:5
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
No protein impact description available
No structure available
Features
Disorder rate (Iupred):
C1=0.175 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF093465=SMI1_KNR4=FE(25.5=100)
A:
NA
C2:
PF093465=SMI1_KNR4=PD(19.0=53.7)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Rat
(rn6)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GAAATGAAGACCACCAGCTAGAGA
R:
ATGCCATAGCTGGTAAAGGCA
Band lengths:
262-1176
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: