MmuINT0005288 @ mm10
Intron Retention
Gene
ENSMUSG00000006204 | 5430419D17Rik
Description
RIKEN cDNA 5430419D17 gene [Source:MGI Symbol;Acc:MGI:1918645]
Coordinates
chr7:131243031-131244871:+
Coord C1 exon
chr7:131243031-131243184
Coord A exon
chr7:131243185-131244653
Coord C2 exon
chr7:131244654-131244871
Length
1469 bp
Sequences
Splice sites
5' ss Seq
GAAGTAAGA
5' ss Score
6.42
3' ss Seq
GCTTTCATCCCCACCCCCAGCCT
3' ss Score
5.66
Exon sequences
Seq C1 exon
GAGGAAGTAACTCTTGTGGAGGAGTCATTTCCAGCCTCTCGGGTTCATTTACGAGTCCACGGTACCCAGAAAACTATCCAACAGACATCCAATGTGTGTGGGAGATCCATGTGGAGAAAAATTTCCGCATAGAACTCATGATTCCGAATTTGAA
Seq A exon
GTAAGAAACTAGTTTTAAAGAGAGGGTTCGATCTGAATAAGAATATTGGGTTTCCTAGCTGTGGTAAGGACATTTTCTTTACTGATTGGAAAAAGCAGAGGAGCACAAAACATAGGAGCATTTCCAAATTCAAGTCTGAATTAATTTTGTAGCAGTACCTAATAGTTCTCTTCTAGCTAGAAAAATGCAGCAAGAATGTTTTGACATAGCTCAGCTTTGGAAATCTGTCTTTTATTTTTTTATTTTTTAATCTTATCTGATCTATTATTTTTATTAATTATTTTACTTATTTACATTCCAAATGTTGCCCACCCTTCTTGGTCCCCCTCCATGAGTTCTTCACCCCATCCCCCCTTCCCTTTGCTTCTGAGAGGGTGCTGTCCCACCCACCCACCCATCCACTTCTGCCTCACCCCACTAGCATCCTCCTTCCCTTAGGCACTAAGTTTTTACAGTGTTAAGTACATCTTTTCCCACTGACCCCTGACAAGTCAGTCCTCTGCTACACATGTAGTGGGGCCCATGGACCAGCCCACGAATGCTCTTTGGTTGGTAACTTAGTCTCTGGGAGCTCAGAGGGTCCCGGGTTAGTTGATACTGCTGTTCTTCCTATGGGTTTGCAATTCCCTTCAGCTCCTTCAGTCCCTCCCCTAATTCTTCTCCACCTATGTTCACATGAAGGTCAAAGGTCATTTCAGGTGTCATTTTTCAGGCACTATTCAACTTGTTTTTCAAGAGAGATTGCTCATTGGCCTTGAGCTCTTAAAGAAGCTAGGTCACCATAACCAGAATTTTCGCATGGGTTCTGGGGACTAAACTCAGGTCTACATGTTTAATGACAAGCACTTTACCCACTGAGCTATTGCTATAGATCCTGGGTTATATGCTTCTAGGCTTTGTCATGCTCCGGCATCACTATAGCTTACAAATGTCTTTACCATCCTCATTAAATATGAGGAAAATGAACAAATGGAGAGTAACTAGCTTGCCCGTTGACAACAGATGCAGGTCTATATGATGTCAAAGCAACAGTTCTTCACCAAAAGGTTTCTTCCAGCAAAATCTTTACAAGGCCTTTCTTCTCTGACATAGCACACACCATGCTGCAATAGAGCAAGATCATGAGATTCCATGATAAACCAGACTCAGCTAGGCCAAATCATGGTTCCATCAGCACTGTGCCAAGGTTGTTAATTTAGATTTGCTTTAAATCCAAGCAATCAGCGATCACAGACTCCTAACATATATTACCTTTGTGGCTGGTCAGAATCACTATAATTTTTAAAATTATGATAAAGTTGTATTAGTAAACTTCATATACTACCTAGGCAAAGAAAATAGAATCCTGATAAAGCATTTGAGAAAGTCTAATGAATACTACATGTTCTGAGATTGTCACATTTTGGGGCATTGATACTGAAGATGTTGCTACTGTGTCATTAACACCCAGCTTTCATCCCCACCCCCAG
Seq C2 exon
CCTGGAAGATATCCTTGGATGTCCCTATGACTCAATTGAGATCTTCGATGGCCCCAGAATTGCATCACTCTCCATGGGGAAGTTTTGTGCCCCATCAGCTGTGGTATTTTTCTCCTCCTCAGACATCTTGACAGTGGTGTTCCGCAGCGATTATATGACAACAAACACTGGCTTTTATGCTTTCTTCAATGCAATTCCACAAGATGGAAGAGAGTCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000006204:ENSMUST00000050586:19
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.038 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0043115=CUB=PU(42.2=88.5)
A:
NA
C2:
PF0043115=CUB=PD(56.9=83.8)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Cow
(bosTau6)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GTGGAGGAGTCATTTCCAGCC
R:
CTTGTGGAATTGCATTGAAGAAAGC
Band lengths:
342-1811
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