MmuINT0022840 @ mm9
Intron Retention
Gene
ENSMUSG00000027580 | BC006779
Description
cDNA sequence BC006779 [Source:MGI Symbol;Acc:MGI:2385169]
Coordinates
chr2:180974190-180975776:-
Coord C1 exon
chr2:180974685-180975776
Coord A exon
chr2:180974374-180974684
Coord C2 exon
chr2:180974190-180974373
Length
311 bp
Sequences
Splice sites
5' ss Seq
TAGGTAAGG
5' ss Score
9.31
3' ss Seq
TGACCTCTTCATCTCTCCAGGCC
3' ss Score
10.11
Exon sequences
Seq C1 exon
GGCTGACGGTTTCAGTACAGCAGCTGCCCAGAAGCCTGGCTCACAATCCTGAAGGACCTGGCCTTTGTCCGAGATGGCATCCGTGGGTTGCAGTCTGAGGTCGGCCAGCACATCCGCCACCAACGGGCCATCCTTAGCCGGACTCTGTGCTAAGGTAGACCTTTACCTGGGCTGCTCCCGCTGCACCCAGTGCCTCAATGAGAGTACCTACATTCTGCGTGAGGTAGAGCACACCTGCCCCAGGGAGATCTTGCTGGCCCGCTTCAAGCAAGCAGCAGAGAGCAAGATCTGGCGTAAGGTGGGCCGCAGGCCTAGCTTCCCAACGCCTATGCGCTATCAAGTCTGTCACTACTATAGGCCAGGGTTGGGCTGTAGGCGTCACTGGAATAGATGCACCTTTGCCCGAAGCCCTGAGGAGGCACTGGTCTGGACATTTGAGCTCAAGAACAACCTTCCCCGATTGAAACTGAAAGAGGCTGTGCAGGGCACCAGAGCCCCAGATAGGCTGCAGACCCCAGCTGACACCATCCGAGCAGAGTTTGGTGGCCACTTCCAACTACTCTGTGCCATCTGCTTCACGTGCTGTCCCCCGTGCCTCTGCCCCGTGGATCCCAGGGGCCATTGCCCTAAGCACCAAATCTGCCCCACACTTCTCATCCATGTTATAGTTGAGGGCCTAAAGCGACAATTCGTGGAGGTGCGGCCACTGCCACAAAGAAGACATCCTTTAAACTACTGCATGTATGTGGGCCGTGGGGTACCATGCCGCCATGGGGCCTCACGCTGTGAGTATGCACACAGTGCTGTGGAGATGGCTGTGTGGAAGGCTGAGCAGTTGGATGGGCTTCAGAGAGGAGATCTGCTCACATATCCTCTCTTTGGGGAAAACAAATGGAAAGCCAGCCCTAACCCTAACCCTCCTGTGACCAAACTGTACTGCCATGCCTGCCTGGTCACCTGTAATTCTCAAGAGGCATTTGAGAACCACTGCTCCTCCCTGGAGCACGCACAGATGGTGGCCTTTGACCAGGCTGTGCCCTGGAAACACCGTGCCCCACCAATGGGACTCTCCAAGTTCGATCTCTGCCCTAG
Seq A exon
GTAAGGAGAATTGTGTGGGAGCCTAGGGTGGGAGAGCCCCCACCCAACGCTAGCCCAAGGGATTGTGAGGTCCACAAGGCCTGAGACCTGCCTATCATTTGCTGTGCCCTCTGCATGTCAAGCTAGTACTGCAGTGGCCTCTGAGGGAGGTTCCTTGTGCCAGCCCTTGTCCTGGATATTCAGGGTACAGAGCAAATAAAACCCCCTACACAATCCATTCCTGCCCCCCATACAGGCCAGGGTTGGGCTGAGAGGGTTGACTCCCGAGGCTGGACATCCCTGAAGTCCTGCTGACCTCTTCATCTCTCCAG
Seq C2 exon
GCCTGATCTCTGTGAGCACGGAGAGGTCTGCATCAAGGCACACTCAAAACAGGAGTTACAGGAGTGGGTTCAGCGGGCACAAGACATGGAACTGCGAGAACAGGCCGCCTGGCAGGATGGGCTGGTACCTTACCAGGCACGACTTCTAGCGGAATACCAGCGCAGCAGCAAAGAAGTATCAGTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000027580-BC006779:NM_183162:2
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=0.012 A=NA C2=0.048
Domain overlap (PFAM):
C1:
PF128742=zf-met=WD(100=7.4)
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Human
(hg38)
No conservation detected
Rat
(rn6)
No conservation detected
Cow
(bosTau6)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TCACGCTGTGAGTATGCACAC
R:
GTGCCTTGATGCAGACCTCTC
Band lengths:
355-666
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: