MmuINT0022843 @ mm9
Intron Retention
Gene
ENSMUSG00000027580 | BC006779
Description
cDNA sequence BC006779 [Source:MGI Symbol;Acc:MGI:2385169]
Coordinates
chr2:180972061-180973318:-
Coord C1 exon
chr2:180972801-180973318
Coord A exon
chr2:180972703-180972800
Coord C2 exon
chr2:180972061-180972702
Length
98 bp
Sequences
Splice sites
5' ss Seq
CAAGTAAGT
5' ss Score
10.08
3' ss Seq
GACCTGTAACTTTCTACCAGGCT
3' ss Score
6.49
Exon sequences
Seq C1 exon
GATCCCTTGCTACATGTGGCCCTACTCAATCAAGAGCCTGGAGCAGCTTTCTCACTGGTGGCCCCCAGTCTCCCACCACACCAGCTCTATGCACAGGGAAAGCACTTCTGTGTACAAAGCTCCCCAGCCCAATACAAGGTAGGGGTGCTTGTGCAGGCTGTCGCCTTCGGCAGCTTTGAGCAGTGGGTGGTCTTTGACTTTGGTCGCAGGCCAGTGCTTCTCCAGAAGCTGAAGTTGCAGCTAGGCCAGACACACAGCCAGGGCCTAAATGGGAAGCCAGCACCCAGCCACCCCCAGGAGCTGGAATGCTGGCACACAGGCAACCGCCACGTGGTGCTTGAGGTAGATTGGACACCCGAGCAGGAAGCCCTGATGGCCAAGTACAAGTTACCCTCCCTGGCCCTGGAGTTCAATCAGATTGTTCCGGACTGGGGGCCCATCTCTCGTTCGAACTACCGACAGAGGATGCACAAATTTCTCTATGAGGAGGAAGCAGCCCAGCAGCAGCTAGTAGCCAA
Seq A exon
GTAAGTGGGGCAGTGGGCTAGCAGGAGTGGCTAAAGTCTGGACTTAGAGATAGGTCTTTGACTATGGCATAGAAAGCTGACCTGTAACTTTCTACCAG
Seq C2 exon
GCTGGCCATGAAGGGCCAGGTATCCCTGAAGACAGCACTGGAGACACCAGCACTCGGCATGCTCTTCGCACCACCAGGGGCCCTCTATGCCAAGGTCCCCTTCCACTCCTCTCTGTTGCCAGACACTGATCAGGGCTTCCTGTTGAGCCGAGCAGTCAGCACAGCCCTTGTGGCTCCCGTGCCTGCGCCTAACAGTACAGTATACCAAGTGCGGCTGGAGGCACGGGCCAGTTCAGACCATGCGCTGTGGCTGCTGTTACCAGCACGATGCTGTATGGCTTTGGGGCTGCAGGCCCAAGACAGCCCCATCTTGGAGGTGCAGTTCCAGATTGACCCTATGACCTTCCGGTTCTGGCATCAGGCAGTGGATGCACTGCTCGAGGAGCACCTGGTGGTTCCTGACCTGCCTGCCTGCACCCTGCCCCACCCCTGGCCCACCCCACCCTCATTTCGTGGCAATCACAAACAGAAGCTGGCTGTGGGGCTCATTGCAGGCAGAAGACCCGAGGGCACAAAGCACATCCCACCACTGCTCATCTATGGCCCCTTTGGCACCGGCAAGACGTACACATTGGCCATGGCCGCACTTGAGGTTGTCCAGCAGCCCCACACCAAGGTGCTCATCTGCACACACACCAACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000027580-BC006779:NM_183162:5
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.104 A=NA C2=0.023
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF130861=AAA_11=PU(53.0=28.8)
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:
TCTATGAGGAGGAAGCAGCCC
R:
CCCTGATCAGTGTCTGGCAAC
Band lengths:
175-273
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: