MmuINT0006230 @ mm10
Intron Retention
Gene
ENSMUSG00000078776 | 9530053A07Rik
Description
RIKEN cDNA 9530053A07 gene [Source:MGI Symbol;Acc:MGI:2442118]
Coordinates
chr7:28157535-28159536:+
Coord C1 exon
chr7:28157535-28158108
Coord A exon
chr7:28158109-28159336
Coord C2 exon
chr7:28159337-28159536
Length
1228 bp
Sequences
Splice sites
5' ss Seq
GCCGTGAGT
5' ss Score
8.56
3' ss Seq
TTGTCTCCTCTCCCTAACAGCTG
3' ss Score
10.7
Exon sequences
Seq C1 exon
GTGACCGTGGACAGTGAAGTGGTGGCACTACCCATGGTTGTAGGATCCATATATATAACCGCTGAAAACCGAAACGTATTTCTGCAGACAAAAAGTGGGCTAAAACTTCTTTTTGATGGCGATGACCATATCCTTATATCCATCCCGAGTCCCTTCCGTGGGCGTCTCTGTGGCCTCTGTGGGAATTTCAATGGGAACCAGAGTGACGACTTTGTGCTGCCCAGCGGAGTGGTGGCCCCCAACGTGGAGGCCTTTGGAGCTGCATGGCGAGCTCCCGGCTCCTCCTTGGGCTGTGGTGAAGGCTGCGGGCCCCAAGGCTGCCCAGTGTGCTCGGCAGAAAAGAGAGAATTGTATGAGGAAAACGATGCCTGTGGGAAGATCCGAGACCCCCAAGGCCCCTTTGCAGCTTGCCACAAGGCTCTGAATCACTCGGAATACTTCCACCAATGTGTTTTTGACCTTTGTACCCATCACGGAGACAGAGACTACCTCTGCCGTAGCCTGGCTGCTTATACTGCAGCCTGTCAGGCAGCTGGGGCAGCAGTGAAGCCCTGGAGGACAGACAGCATCTGCC
Seq A exon
GTGAGTGTCTCTGACCCCTTGGGTGACCCCAGGCCCTCCTTTCCTGTAGAAGTCCCTGCCTGTAACAGGGTTTCTTCCAGCCCTGCCCTGCATCCTCTATGGCTTTCCTCCTTTCCTTCTGGCTCTGGGGTCTCAGACTCCAGTCAAGAGTCCACACTCCCCAGCCTCGACATTCACCTTTTCCCAGGGCTGTTCCCAGCTCTTTCCATACTGACCTGAAATGGAGTTGGGTGGACTGAGAGCCCACGGGAGTCCTGAGTCTCACAGTCACTGGCCCTTCCCACAGACTCTGTATTTTCTCACATCCTCAGTGCAAGGCCAGAGGCAATAGATGCCCCCCCCAACTACACACCTATTTCCAAATTATTGGATAACAACAAGTCCCCTCAGATGCCCCGTGCCAAAGCAATGGTCCTTAGCACTTTAGTAAAGAGCCTTTTCTCCTTCAGTTTCCTATTAATACCTAGACCCAGAGTCCCATCAGCTACCCAAAGGAACTGAAAGAGTCCCAGTTTGACTGTGGACACCATCACTAGCTCAAACAGTAGGCTAGGTCATGCACTCTGTGCTCTCTGAGCTTACCCTGGTGGCCCTCAAGGTCTCTGCACCAGCCGGATTTCCAACTGAAATCAAACTTCACCCCAAACCTGATTCTCCTTTCCTGCCCCAGTTATTATCTGATGGTAGCCACACCCGTCCGCAGCACTAAGCCAGAGCCTAATCTTTGATGTCTTCCTGTGTCTTTCACATATCCTTGTCTTTCCCTTGCCCCATCCTCAAACCCATTCTTGTGCTATCCCAACCCTTTGCACACACCTATCCGCTCACCTAGATACTCTGCTTTCCCCTGTCCCAAGTGAACCCTGTCAGAGCCTCCCCGGGTCATCCATCCCATCTGCCCGAGCCTCCCAGTGCATCCGAATCTTCTGCCTCACTTCCCTGGCCCATCCTGACAGCCTGCTTGTCCGCTGCATCCCATCCTCAGCCTCCTCATCCCATCCCTGTCTCCTGGCTGGTCCTTCAAGGCCAAGCCTCGCCTTCTTCCGTTAGCATTTCCATTTCCCAGGCCTGACACTCTCCTCTCAGATGTCTCCTCTCCCCAGCCCCTATACCTCTTCTCTCCCAGTGCAGTATGGCAGCTGTAACTGTCTGTATACCTGGATGTGAGTTTTGTAAGACAGGGTTGGAGACTGCCTGCCACATTCACCTTGTCTCCTCTCCCTAACAG
Seq C2 exon
CTGCCGAGTGTCCTGCCCACAGCCACTACTCTATCTGTACACATTCCTGCCAGGGCTCCTGTGCTGCAATCTCTGGCTTCACTGGCTGCACCACGCAGTGCTTTGAAGGGTGTGAGTGCGATGACCACTTCCTGCTCTCCCAGGGTGTGTGCATTCCTGCCCAGGACTGTGGCTGCTTCTACAATGACCAATATATGCCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000078776:ENSMUST00000150948:15
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:
PF0009420=VWD=PD(52.1=39.6),PF087426=C8=WD(100=39.6)
A:
NA
C2:
PF087426=C8=PD(0.1=0.0),PF0182612=TIL=WD(100=80.6),PF127142=TILa=PU(16.4=13.4)
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:
TGAGGAAAACGATGCCTGTGG
R:
CAGGAAGTGGTCATCGCACTC
Band lengths:
355-1583
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