MmuINT0005547 @ mm9
Intron Retention
Gene
ENSMUSG00000015488 | 5930434B04Rik
Description
RIKEN cDNA 5930434B04 gene [Source:MGI Symbol;Acc:MGI:1924317]
Coordinates
chr2:26869613-26871129:+
Coord C1 exon
chr2:26869613-26869685
Coord A exon
chr2:26869686-26871003
Coord C2 exon
chr2:26871004-26871129
Length
1318 bp
Sequences
Splice sites
5' ss Seq
GATGTGAGT
5' ss Score
7.77
3' ss Seq
TTCTGCCTTTGACCCTGCAGCAT
3' ss Score
9.26
Exon sequences
Seq C1 exon
CCTGTGCCATCTCTGGACTCTTCAACTGCGTCACTATCCACCCTCTGAACATCGCAGCTGGCGTGTGGATGAT
Seq A exon
GTGAGTAGCTGTGAATGTCCTGCCTGGGTGGGGTTTGAGACATGTGGTGCAGGTCTCATCCCCCTTCCCGCTCCTAGGTTTCCTGACAGCCGCTTAAGTCTTTATTGGGGACAGTGTCACAGATACAGTTGCAGCCTCTACCCAGCCAGACACTGTAGACTCCTTGGGAGCTTCAGGGCCATGGTGTGTAAGGTCAGAATCCAGGGTCTGTGACAAAGAGAGGAGGGTGGTCAGCTGTGAGGCCATTAGCAGGGCTAGAGTTGTGGGGGGAGGGGTCAGACGCAGGTGGACCTGGTGGCTACAGCATCCACAGGGAGTTCCTTTTCATGCTCTTCCTGGGCAGCCAGATCCTGGGGAAAGGGATGCCAGAGTGAGGGCTGCTTGAGGTGCATGGAAAGCACTGTACATTAGCACTGTATAAACAGTCATCTTGGGCAAGGTATAGGTAGGTCTTGCCTTGGGCATCATGAGGGTCAGGATGACTTGGATCTTAGGGTGATGTGTACAGAGGCTTATGCTGGCCCAGGCAGCAAGGATGGGGACTATAGAGGTTATATACACATTGGTGGAAAGTGAGCTGGCATCTGGAAGACTGGTGATGGGTGGTGGGGAGATGGGCAGTGGTCAAGAGTTCCAAGAGCTGTGTCTGTTAATCAGGTGGTTGGTGGCACTTTGCTCCCAGATACATGTGGGGCCCGGCAATGATCCTGTTGTCTGGTCATGACCATTGCCCGCCTATGGGAGCAAAGGCCTTGAGCACCAGCAGCATAGCTGCTTCCAGCAACCAGGCAAGGGTTAAAGGTTCCTGAGTGGACGCTCCCAGCATGAGCAGCCCACTACCTGCATCTCTGTCTCCCTGACCCACATGCTCCCAGCTCAGGCCATGGGTAGTCCTCGGTGGCTCGGTACCTTGCACTTCTGCTGGGGCCAGCCTATCCTTGATGTCAGTGTTCGTGACTATGGGGAAGGGCCTAACAACAGGCAGTGTGGCTAAGTTCTGCGGATGAAGGTGCTGCTGGCTAAAGATTATATGGAACCAAGGGTCTTAGTTCTTCCTTTCACTGTTGGAACAATAAAGAGATCAGACACCAGGCTCTTCCTCCAGGATGCTTGGGTAGTTAGGGATGCTGGTGCAGCCGTGGGGTGGCGTGGGGCGGGTTGTTGAACTGCTTGGCAGAAACTGGTACCCTGCAGAATCCAGGTGTTTATGGAAGTTCAGGGCCTGTGAGGTGGTAGAATTCCTTGAGCCACTGGCATGAGGGCTGTTGTAGCCTCAGGTTGTAAACTGTCATTGTCCTTTCTGCCTTTGACCCTGCAG
Seq C2 exon
CATGAACGCCTTCATCCTGTTGTTGTGCGAGGCTCCCTTCTGCTGCCAGTTTGTGGAGTTTGCAAACACAGTAGCTGAGAAGGTTGACCGGCTGCGCTCCTGGCAGAAGGCTGTCTTCTACTGCGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000015488-5930434B04Rik:NM_029862:2
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:
PF085075=COPI_assoc=FE(35.3=100),PF102334=Cg6151-P=FE(30.8=100)
A:
NA
C2:
PF085075=COPI_assoc=PD(37.7=59.1),PF102334=Cg6151-P=PD(56.8=95.5)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CCTGTGCCATCTCTGGACTCT
R:
CCGCAGTAGAAGACAGCCTT
Band lengths:
199-1517
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: