MmuINT0003185 @ mm9
Intron Retention
Gene
ENSMUSG00000030385 | 2900092C05Rik
Description
RIKEN cDNA 2900092C05 gene [Source:MGI Symbol;Acc:MGI:1920340]
Coordinates
chr7:13139967-13141670:+
Coord C1 exon
chr7:13139967-13140124
Coord A exon
chr7:13140125-13141361
Coord C2 exon
chr7:13141362-13141670
Length
1237 bp
Sequences
Splice sites
5' ss Seq
CAGGTGCTT
5' ss Score
4.83
3' ss Seq
ATATAATTTCTATATTTTAGTTA
3' ss Score
6.8
Exon sequences
Seq C1 exon
TCGACTGGTAAAAGTTGAGGAAAAACAGCAGCTTGCAATGTTGTATGAAAATATCGAGATTCCACTTGTAGATGAGAAAGAGGCCTCTGAAGATGATGGTTATGATGAATCTCAGTTGCATCCAGAGAATGAGGAGCTGGGAAAATTCATTAGCTCAG
Seq A exon
GTGCTTTTTCCTATTATATCCAAGGCTGTCAATGGTGATTTGCTCTTTTCCAAAGAATATTTAAGTGGGATCAAATATAATCTGAGTTAGGAAAAAAGGATGTTCATATAGAAATGAGCCATTCTTATCAAATCCCAGGGGACAATGAGGAGCTGTCTTGTTGATTCCCAATGTGGACAATTCCAAGAATCTAAGCCAGACTTTGGGAAACAAATCTTGTTTTGAATGAAACTTTACCTTGAACATAATTATTATTGTTGCAGTATTCCTGCATTTAGAATATCTACAAGCAGACACTCTCATTTGCTTCAAGATGGTATAGAAATGGGTTCCAGGTCTGTACAATAGAGATCATTTCTCCCAAATGGAAGGACACTATGTGAGACACAAGCATATGAGAGATGACTATGTGCATTTGTGAAGAGAGGATGTCATAAATTCTCCAGAAGCTTGGTTTTGTAAAAAAAAAAAAAAAACTTTCAGGTTCCTGATCATATGTTCTAGAAGAACACGTAATGTTCAGTGTCTGATCCAAACACAATGACATCCTCTGCTTGGTTCCTTTTAAACAACCCTAGCCGGGCGGTGGTGTCGTGCGCCTTTAATCCCAGCACTTGGGAGGCAGAGGCAGGCGGATTTCTGAGTTCGAGGCCAGCCTGGTCTACAAAGTGAGTTCCAGGACAGCCAGGGCTACGCAGAGAAACCCTGTCTGGAAAAACGAAAACAAAAACAAACCAACAAACAAACAAACAAACAAAAAACCAACCCTAGATGTGCCCAACCTGAAAGACTCAGATGCTAAGAGCAGAAGTAATGGTTGATGCTGCCTGAGGTTAAGCCTTTATAACCTGTAAAATAATATTTTCCAATGCCTTTTTAATTACATTGAATTATTATTGGATAATTGAAAGGCTTGAATACAAAATATAATCATATTCAAATTCAAACTTTAGCTGAGGGTGATGACTCACACCTCAACTCACAGCACTTGGGTAGCGGTAACAGGCAGATGGTGAATTCAGGGCCAGCCTGGAATGTATAGTATGATCTTGCTCCAAAATTCAAACAAACAAACAGAAAAAAATACATATTATTAAAAAAAAATCACCATCCTTATAAGTAACATTTAGTATTTTTTTGAAATACCTTTATTTTTTTCTGATTTCCCCTAACCCCTTTGTCTTCATTTCTGACCTTCATTTACTCCAATCTTAGTAATATAATTTCTATATTTTAG
Seq C2 exon
TTATTAAAACAAAAAGAATGGAAAACTTAAGAAGAAAATGAAGGAAGAGCAAAATGTATTGAAGACCATCAGAGAACTCCAGTTATACCAAAAAAGTGGAGTCATGAAAAAATGGAGAAAGATGAAAACTCAGGAAAGCTGTGAAAACAAAAGAAAGGTGTACCATGTGCTAGACAATGTAGAGACCAAACTGAAGAGATAACAGACAACTGAGAACACAAACAGGACTTCTAGAGAACTTGTTCAAGAATGTTCTACATAAAGAAACATGAGAATCATATAGCAGAAAATAAATTCATATAATACCAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000030385-2900092C05Rik:NM_028434:5
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.185 A=NA C2=0.077
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
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GCAGCTTGCAATGTTGTATGA
R:
TCCTGTTTGTGTTCTCAGTTGTCT
Band lengths:
358-1595
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: