Special

MmuINT0005467 @ mm9

Intron Retention

Gene
ENSMUSG00000054672 | 5830411N06Rik
Description
RIKEN cDNA 5830411N06 gene [Source:MGI Symbol;Acc:MGI:2443685]
Coordinates
chr7:147482185-147482898:+
Coord C1 exon
chr7:147482185-147482502
Coord A exon
chr7:147482503-147482583
Coord C2 exon
chr7:147482584-147482898
Length
81 bp
Sequences
Splice sites
5' ss Seq
CGGGTGAGT
5' ss Score
9.89
3' ss Seq
CTGACTGCGTCTCTCCACAGGGA
3' ss Score
11.66
Exon sequences
Seq C1 exon
GTCTCCAGGATGCCCTTCGGCTGAGGGAGGGACAGAGTCACTGTGATGGCCGAGTGGAGGTCTTCCTGGATGGCACGTGGGGTCGTGTGCTGGACAGTGCATGGGACCTGCGTGATGCTGCTGTGGTGTGCAGGCAGCTTGGGTGCGGAGAGGCACAGCTAGCCTATGATGCGCCAGCACCAGGCCATAAGACCATTCCTGTGGGGCTGAGTCTGGTGCACTGCTTGGGCTCTGAGACCCACCTGACCCAGTGCAATGTATCTGCTTCTCTGCTGGTTCATGCAGGGACTTTGCGGGATGCAGGAGTGGTGTGCTCGG
Seq A exon
GTGAGTGTGAGGTGTCCACTTGCCCACCCCACCCTGCTCTGTTCATGTAGTCCAGTGTGTTCTGACTGCGTCTCTCCACAG
Seq C2 exon
GGAGCTTGCACATACGGTTGGCAGCGGGTAAGAACCGCTGTGCTGGGCGTGTTGAAGTATTCTATCAGGGCACATGGGGCACCGTATGTGATGATGCCTGGGACCTGCAGGATGCCCATGTGGTCTGCAGGCAGCTGGGCTGTGGTCATGCCCTCAGTGCCCCTAGGGCTGCCCACTTTGGAGCAGGAACTGGGCGCATCTGGATGGATGAACTGGGCTGCATGGGTGAGGAGGCTGCTCTATGGGAGTGCCAGTCAGGAGGCTGGGGCCAACAAGATTGTGGGCACAAGGAGGATGCAGGCGTCATCTGTTCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000054672-5830411N06Rik:NM_001128145:6
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=91.6)
A:
NA
C2:
PF0053013=SRCR=WD(100=92.5)


Main Inclusion Isoform:
NA


Main Skipping Isoform:


Other Inclusion Isoforms:
NA


Other Skipping Isoforms:
Associated events
Other assemblies
Conservation
Human
(hg38)
No conservation detected
Rat
(rn6)
No conservation detected
Chicken
(galGal4)
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CTGAGTCTGGTGCACTGCTTG
R:
ATACTTCAACACGCCCAGCAC
Band lengths:
172-253
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