Special

MmuINT0005466 @ mm9

Intron Retention

Gene
ENSMUSG00000054672 | 5830411N06Rik
Description
RIKEN cDNA 5830411N06 gene [Source:MGI Symbol;Acc:MGI:2443685]
Coordinates
chr7:147481739-147482502:+
Coord C1 exon
chr7:147481739-147482044
Coord A exon
chr7:147482045-147482184
Coord C2 exon
chr7:147482185-147482502
Length
140 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGT
5' ss Score
10.67
3' ss Seq
TCAGAGTTTCTCCCTGTCAGGTC
3' ss Score
6.9
Exon sequences
Seq C1 exon
AGTTCCGACTGGTCAATGGCAGCAGCCGCTGTGAGGGCCGCGTGGAGCTTTTGGTACAGGATGCCTGGCAACCCCTCTGTGCTGCCAACTGGGACTTAGCAGATGCCACTGTGCTCTGCCACCAGCTCAACTGTGGCTATGCAGTGGCCACACCGCAAGGAGGCCACTTTGGAAATGTGGAAGGTCCCATCAGGACAGATGTGTTTCACTGTGTGGGAACAGAGCCCCACTTACTGAGCTGCCCAACAAGCACCTTAGGGGCCCAGGCATGCGCACTGGGGAATTCAGCCTCGGCTCTCTGCTCAG
Seq A exon
GTGAGTGCAGGCAGCCTTGAGACTGCGAAGAAGAAGGTAAACAGGACGAAGGTAAACAGTATGAGAGATTTGGGAGGGTGAGGATAGGTGGAGATGTTCGGAGCGATGGTCCTCTGCCCATCAGAGTTTCTCCCTGTCAG
Seq C2 exon
GTCTCCAGGATGCCCTTCGGCTGAGGGAGGGACAGAGTCACTGTGATGGCCGAGTGGAGGTCTTCCTGGATGGCACGTGGGGTCGTGTGCTGGACAGTGCATGGGACCTGCGTGATGCTGCTGTGGTGTGCAGGCAGCTTGGGTGCGGAGAGGCACAGCTAGCCTATGATGCGCCAGCACCAGGCCATAAGACCATTCCTGTGGGGCTGAGTCTGGTGCACTGCTTGGGCTCTGAGACCCACCTGACCCAGTGCAATGTATCTGCTTCTCTGCTGGTTCATGCAGGGACTTTGCGGGATGCAGGAGTGGTGTGCTCGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000054672-5830411N06Rik:NM_001128145:5
Average complexity
IR-S
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:
PF0053013=SRCR=WD(100=89.9)
A:
NA
C2:
PF0053013=SRCR=WD(100=91.6)


Main Inclusion Isoform:
NA


Main Skipping Isoform:


Other Inclusion Isoforms:
NA


Other Skipping Isoforms:
Associated events
Other assemblies
Primers PCR
Suggestions for RT-PCR validation
F:
ACTTAGCAGATGCCACTGTGC
R:
GTGACTCTGTCCCTCCCTCAG
Band lengths:
254-394
Functional annotations
There are 0 annotated functions for this event


GENOMIC CONTEXT[edit]

INCLUSION PATTERN[edit]


SPECIAL DATASETS

  • Pre-implantation embryo development
  • Muscular differentiation time course
  • Spermatogenesis cell types
  • Reprogramming of fibroblasts to iPSCs
  • Hematopoietic precursors and cell types