MmuINT0006132 @ mm10
Intron Retention
Gene
ENSMUSG00000056004 | 9330182L06Rik
Description
RIKEN cDNA 9330182L06 gene [Source:MGI Symbol;Acc:MGI:2443264]
Coordinates
chr5:9461322-9463034:+
Coord C1 exon
chr5:9461322-9461500
Coord A exon
chr5:9461501-9462868
Coord C2 exon
chr5:9462869-9463034
Length
1368 bp
Sequences
Splice sites
5' ss Seq
AAAGTAAGT
5' ss Score
9.72
3' ss Seq
CTCTATCTACCCCTGCTTAGGCT
3' ss Score
6.54
Exon sequences
Seq C1 exon
GAAATATTATATGTATGGAATGAACCTAAGTGGTGCATTAAAGGAATTTCTTTGCCCGAAAAGAAGTTGTCAACCTGCGAAACTGTTGACTTTTGGCTGAAAGTGGGAGCTGGTGTGGGCGCGTTCACAGCCGTTTTGTTGGTGGCTTTAACATGCTACTTTTGGAAAAAGAATCAAAA
Seq A exon
GTAAGTAACCTCATTAAATGATCTTATAAGAACTGGAATGTCTGTTTATACTGTGAGAATTTTAGATATAATGGTTGTATGTTATCCATTCCATCAGTGCCATGAGGCATTTCTGGTAAGGAAGGTAGGTATAGGCAAGGCATTTGAGAAAATAGAGAGAATAAAGGATTCTTATTTTGATAATTGAAAGTGGAGAGAACATTACTGACCACTGGATTAGTCATTTGTTCTAAAAATGAAACACTCTCTAAGTTACCCAGATAGGAACAGAGCGGAGATTGGAAGGTGACATAACTTCTTTCTCTGACATAATCTGACTTCTTGTTGTATCAGTTTCACTTACAAAGATGTTTTTAAACAAATAGACTAAGCAAATTGGCAAATATCAGATTTATTTATCCCAAATCTCAAAGACTCTGCTGCCAAAAGTTGAGTCCAACCCTTTTGTGCATCTGTTTCTTGGCTTGGATCATGACTTGAATCTTTGGATTCAAGTGCAATGTGGCAGATCTATGTTCTATTTTCTAGGAATAATTATAATATCTGATGTCATAACTAAAGAGAAAAAGCCCAAATGAAGCAGAGATATAGTAACAAGCAAATCATCTGCCCAATATTCTCATCTTCATGATCTGAACCTTAGAAAACGTGATAGGGAATTGATATCACATGAATACACTAAGGAAAGGAAGGAAAGGCATTCTGGCATTAAGGCTTTTCTTTGTTTTATAAATGTTCTTTTTTTTGTAAAGATTTATTTATTTATTTTATATATGTGAGAACACTGTAGCTGTACAGATGGTTGTGAGCCTCATGTGGTTGTTGGGAATCTTAGGACCTCTGCTTGCTCCTGTCAACCTCGCTCACTCTAGTCAACTCTGCTTGCTCAGTCCCTGCTAGCTCCGGCCCAAATTTACTTATTATTATACATAAGTACACTGTAGCTGTTTTCAGACACACCAGAAGAGGGCGTCATATCTCATTATGGGTGGTAGTGAGCCACCATGTGGTTGCTGGGATTTGAATTCAAGACCTTTGGAAGAGCAATCAGTGCTCTTACCTGCTGAGCCATCTCACCAGCCCCATAAATGTTCTATATAATTAGTCAGTAAGGTCATTAATGTAAGTGGTAAAATTAACTCTATTGAACTGATTCTCTGACATCTTGTGGAATATTTTTATGTATTTAGTTAATAAGTGAGAACATTTAAAGCTACAGCCACAGATGAGGCAAATATGCTGTTGGAAAAACTATGCAGGACTATCAGAACTATTTTAGAAGCTGGTATAATGTTTATAATAAATATGAATGTATTATTACTATAAATGGTTATATAACTATTTACTTCTCTATCTACCCCTGCTTAG
Seq C2 exon
GCTGGAATACAAATATTCTAAATTAGTAATGACGACTAACTCAAAAGAGTGTGAACTCCCAGCTGCAGACAGCTGTGCTATCATGGAAGGAGAAGATAATGAAGAGGATGTTGTATATTCCAACAAACAGTCACTACTAGGAAAACTTAAGTCTTTGGCCACAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000056004:ENSMUST00000069538:20
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
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:
CCTAAGTGGTGCATTAAAGGAATT
R:
TGTGGCCAAAGACTTAAGTTTTCC
Band lengths:
318-1686
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