MmuINT0023238 @ mm9
Intron Retention
Gene
ENSMUSG00000047228 | BC048546
Description
cDNA sequence BC048546 [Source:MGI Symbol;Acc:MGI:3039594]
Coordinates
chr6:128530961-128531624:-
Coord C1 exon
chr6:128531466-128531624
Coord A exon
chr6:128531145-128531465
Coord C2 exon
chr6:128530961-128531144
Length
321 bp
Sequences
Splice sites
5' ss Seq
ACCGTAAGG
5' ss Score
6.08
3' ss Seq
TGGCTGTTCTCTTTGTGCAGGCG
3' ss Score
9.04
Exon sequences
Seq C1 exon
AGAGGGAAAGAAAGTGGGATGCCTAAGAAACTGGCCAGTAAGAGGAGGGAAAAGACAACTTCTTCTAAAGTCACCCTCCAGGTGCTGGGACAACATGGTGCCTACCATCTTGCTCAGTGCCCTCCTGCTTCATTTCACTGATGTTGTGGCTGCAGAACC
Seq A exon
GTAAGGGAATTCTAATCTCTCCGTATCCAAGTACTGACAATATCGTTTTGCTAAATGGATTCCATGTTAAAATCTAGCTGGTTCATTATTCTATTTCAACTACAGCAAGTGAGTGCTGGTCTGCCCTCTAAGGGTTGAGCAAATGCCAGATGGATACTATATTTTTAAGACACCACTGTGTGCATCTGGTTTATCATTATGCTACCTGTTAAAAAAAAAAAAGCACAGTTTGGGGGATCCTTCAATACTCAAGTTGCTGTGTGTGAATGCAAACAAGTCTCTAGACTTGTTTGCCAAGTGTTGGCTGTTCTCTTTGTGCAG
Seq C2 exon
GCGATACATCCTGTGGGTTTCTTCCGTGGTACAGCGATTTTCCTCAGAAAAAGCCTGTCTTCATCTTTTAAACCTCAACGAATCTGTGTCCTTGAGCGTCACCCTAGAATATGATGGATCCAGTACTACTATTTTTGACCAGCCCGTGGACGAGGGGAACTTCTACGCTTGTGCAGATTTCAAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000047228-BC048546:NM_001001179:1
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
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
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Rat
(rn6)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GAGGGAAAGAAAGTGGGATGCC
R:
TTTGAAATCTGCACAAGCGTAGA
Band lengths:
342-663
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
Other AS DBs: