MmuINT0005285 @ mm10
Intron Retention
Gene
ENSMUSG00000006204 | 5430419D17Rik
Description
RIKEN cDNA 5430419D17 gene [Source:MGI Symbol;Acc:MGI:1918645]
Coordinates
chr7:131237966-131239548:+
Coord C1 exon
chr7:131237966-131238283
Coord A exon
chr7:131238284-131239515
Coord C2 exon
chr7:131239516-131239548
Length
1232 bp
Sequences
Splice sites
5' ss Seq
CAGGTATTC
5' ss Score
6.49
3' ss Seq
GTTTCTCTTTCTGTATACAGATT
3' ss Score
9.17
Exon sequences
Seq C1 exon
GAGACTGGCCAGAGCTTCGCCTAGTGGGTGGTTCCAGTCGGTGCTCAGGACGAGTGGAAATCCTCTACCAGGGAGTCTGGGGCACCATATGTGATGACCTGTGGGGTTCAAATGAAGCTGAGGTTGTATGCCGCCAGCTAGAGTGTGGCCAGGCTGTTTCTAGCCTTGGTGAGGCTTACTTTGGCCCAGGCTCTGGAGAAATCTTCCTAGACAACCTTCAGTGTTCTGGAATGGAACATTACCTCGGCCAGTGTCCACATTCTGGATGGTCTGAACATAACTGTGGCCACCATGAGGATGCTGGTGTTATCTGCTCAG
Seq A exon
GTATTCATTCTCTTCCTATGCAAATGGAGGAATTTGGAAACTATCTTTTTTGAGTGAAAATTTCCAGCCACCCATTTGATTCTTTAAGCAACCCTTCAGGACCAGGTCCTAGGTGCAGACACCTACCCTGTCATGAGTAGCACTTGGTGGTTATGGGAAGTCTACGATATCTATTGGCACCACTCTGGGGCATTGCAGTAAGGATTCCAGGGTCGCTCTCTTAAGAAACTACCACTGAGTAGGTTTGGGAAGGAGCTCTGGAGCCTGCACTTAAAGAGTTCTCCAGGGGTTCTGCATAGGGGTATCACAAGTACCTAGCTCTGCCCACCATGAGACATAACCTACCTAGTGGCTGGTCTAAGTTTTCTTTTTTTTCCCATTTTTTATTAGGTATTTAGCTCATTTACATTTCCAATGCTATACCAAAAGTCCCCCATACCCACCCACCCCCAATCCCCTACCCACCCACTCCCCCTTTTTGGCCCTGGCGTTCCCCTGTACTGGGGCATATAAAGTTTGCGTGTCCAATGGGCCTCTCTTTCCAGTGATGGCCTACTAGGCCATCTTTTGATACATATGCAGCTAGAGTCAAGAGCTCCGGGGTACTGGTTAGTTCATAATATTGTTCCACCTATAGGGTTGCAGATCCCTTTAGCTCCTTGGCTACTTTCTCTAGCTCCTCCATTGGGAGCCCTGTGATCCATCTAATAGCTGACTGTGAGCATCCACTTCTGTGTTTGCTAGGCCCCGGCATAGTCTCACAAGAGACAGCTACATCTGGGTCCTTTCAGCAAAATCTTGCTAGTGTATGCAATGGTGTCATCGTTTGGAAGCTGATTATGGGATGGATCCCTGGATATGGCAGTCACTAGATGGTCCATCCTTTTGTCACAGCTCCAAACTTTGTCTCTGTAACTCCTTCCATGGGTGTTTTGTTCCCATTTCTAAGGAGGGGCATAGTGTCCACACTTCAGTCTTCATTTTTCTTGAGTTTCTTGTGTTTAGGAAATTGTATCTTATATCTTGGGTATCCTAGGTTTTGGTCTAAGTTTTCTAAGCCAAGAATTTACCTTAGATGAGGGTGTCCAATTGGTGGTTCTAGGAGCTAATTTCTGTACCCAGATAGGCCATGAGTCTGTCCCTCTTACTCACCATCCCCTTCTTGTCACCCCATCTTCCATCCTTTGAGGTCGTCAGAGAGAGTGACCTGTTGTTTCTCTTTCTGTATACAG
Seq C2 exon
ATTCAGATGCCCCTCCTCCACCTATGCCGCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000006204:ENSMUST00000050586:16
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.019 A=NA C2=1.000
Domain overlap (PFAM):
C1:
PF0053013=SRCR=WD(100=91.6)
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:
GAGACTGGCCAGAGCTTCG
R:
CATAGGTGGAGGAGGGGCATC
Band lengths:
344-1576
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