MmuINT0054793 @ mm10
Intron Retention
Gene
ENSMUSG00000078580 | E430018J23Rik
Description
RIKEN cDNA E430018J23 gene [Source:MGI Symbol;Acc:MGI:2141981]
Coordinates
chr7:127393001-127393619:-
Coord C1 exon
chr7:127393253-127393619
Coord A exon
chr7:127393115-127393252
Coord C2 exon
chr7:127393001-127393114
Length
138 bp
Sequences
Splice sites
5' ss Seq
TGGGTGAGA
5' ss Score
6.04
3' ss Seq
TTTGCTATCTTTCCCTCCAGAAG
3' ss Score
10.61
Exon sequences
Seq C1 exon
GTTCATCACCACGTCTTGCATCTGTACCTGCTTCTAGGAATCTTCAATTTTCACCTACATTAGGGTGCTCACGGACCTGATATATGTCCTTTCTCAGCCCTGGTACCCCACCGCGGCAACCTAGGATCTGGCAGGCGATCCAGGGGACGCCAGGCAGATCACGGAACAGTGCGGGGAGTCCCCATGGCGCCGCGGATGGCCCCGGAAAGGGCCTCCGCTTGGCCTGCATTCCTTAAGCCTGGGACTGTGAGCTTCGCGGACGTGGCCGTGTACTTCTCCCCGGAGGAGTGGAGGTGTCTGCGGCCGGCGCAGAGAACCCTGTACCGAGAGGTGATGCGCGAGACCTATGGTCTCCTGGCCTCTCTGG
Seq A exon
GTGAGAACCTTCCTGGCCGCCTGGGTTCGCGTAGCCCTTGACACTGTGGGTCATGCGGTGGATCGGAGTTCCCTGGGTACGGGTGGTCGTAACAAGTGGGTCGACCTGACTCGTGGGGTTTGCTATCTTTCCCTCCAG
Seq C2 exon
AAGTCGGGGGCGACAAACCAGCGCTCATCTGCTGGGTGGAGGAAGAGTCCGAAGTGTGGGGACCCGGTGCCCAGGAGCCAGAGGTGGCCATGTGCAGGACAGAAGTCCACTCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000078580:ENSMUST00000165495:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.032 A=NA C2=0.491
Domain overlap (PFAM):
C1:
PF0135222=KRAB=WD(100=66.1)
A:
NA
C2:
PF0135222=KRAB=PD(0.1=0.0)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CCTGCATTCCTTAAGCCTGGG
R:
GACTTCTGTCCTGCACATGGC
Band lengths:
252-390
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