MmuINT0005177 @ mm9
Intron Retention
Gene
ENSMUSG00000040412 | 5330417C22Rik
Description
RIKEN cDNA 5330417C22 gene [Source:MGI Symbol;Acc:MGI:1923930]
Coordinates
chr3:108268524-108270934:-
Coord C1 exon
chr3:108270671-108270934
Coord A exon
chr3:108268698-108270670
Coord C2 exon
chr3:108268524-108268697
Length
1973 bp
Sequences
Splice sites
5' ss Seq
AAGGTGCCG
5' ss Score
5.74
3' ss Seq
CTGGATCCTCTCCCCCTCAGATC
3' ss Score
9.41
Exon sequences
Seq C1 exon
GGCAGGAAGTATACTAATGATGTCGCCAAGATCTACTCAATCAATGTCACCAACGTCATGGGGGGCGTGGCCTCCTACTGCCGTCCCTGTGCCCTAGAAGCCTCTGATTTGGGCTCCTCCTGCACCTCTTGTCCTGCTGGCCATTACATCAACCGGGATTCTGGGACCTGCCACCTCTGTCCCTCTAACACCATCCTGAAAGCTCACCAGCCTTACGGTGCACAGGCCTGTGTGCCCTGTGGTCCAGGGACCAAGAATAACAAG
Seq A exon
GTGCCGGGTTCTAAGTGGAATTCTCCAGGGGCTGAAACCCATATGGCCCCCCTTAAACACCCCCACCCCCAGCCCCACACTCAGGTTGTTGTGGAGGACACTAACCAGGAGGTGTCTGTGGGTGGTGAGTCCATAGCAGGAGGTCTTGTCTTCCCTCTGTAGCAGGCAAGTCACATTTTCAGTTGGTGGAGATCAGTGACCCTGTGGTCCAGAGGTTTGGCATCTGTGCAAAGACCTGAAGGGAAGAAGTAGTGGGGGTCTGTGGCCCATGTTTAGCTCATTAGCACAGTAATCTGCCCCCTCTGTTTTAGGAAGGTGAGCCAACCTTTGCTGGTACCTACAGTTAATCAGCATTGCTGCCATCCATCCAAGGGGCTTCTCAGCTCTACGGATAGAAGAATCTAGTGTGGCCCAACAGTGACACTGCCCCCAAGTAGTTTTGCATCCATGCGCATACATGTACATGGTGGCTCCTATCAGTAATCCCTCACTTGGGAGGTAGAGGAGAGGAAGTCAGGAGCTCAAGGTTACTCTTGTCCTACACAGCAAGTTTGAGATCAGCATAGAACTCATGAGACCCTGTCTCCAAAACAAACAAACAAACAAACAAACAAACAAAAAGATAAAACCCCAAACAAAGTACATATGAAGAAAGGCTCTTAGATAGTTGTTAACATTTAGAATTAATTTGTATTTTGACTGCTCACACCAGAAAGACACCTATAAGATGTTATTCATTTATTTAAATTTATTTATGTATTTATGAGACCAGGTCCCATGTAGTCCAGACCAACCTCAAACACTATATAGTCTTGCTCTATTTATCTGCAAAGGGTGTACATTCATTGTACAGACCCCTGAAAATTTTTTAGGGCAGTGGTTCTCCAACTGTTGAGTGGGAGTGGCATGCCAGATATCCTGCATATCAGATATTCACGTGACAATTTCTAATAGTAGCAACATTACAGTCATGAGGTAGCAATCAAGATAATTTTATGGTTTGGTGTCTTAAAGGATCTTAAAGGGCCACAGCAGTAGGAAGGTTGAAGACCACTCACTGTCTTAGGGTTCACCTGAGACGTTCTTCATAGTCTTTCCCTGGAGCGCCCTCTGCTGGTGGGGCAAGGGGAGAATGGCAGTATGTCAGACTGCCTGCCTCTGACTGGGGTCTCTGACACAAGGACCAGGAAACAAAGTTCCTTCCATAGTTGGGTTTCCTACAGAGAACTCCAGCAAAAGGAAGGAAGTTTCAGTGTGTTTGAAGTGGGCATGTGTGCGCCGCATAGGCGGGGAAGAATAGAAGCCTCTTTCTTGCCACTCAGAAGCCCTTATTTCAGTTAAGGCTCTGCTGTCTTCTGCTTGAAAGACAGGGTTGGTCACAGAGCACATGCCCAGCCTGCACAAGGCTCTAGGTTTGGTCCCTAGCCCTATTAAAAACAAAATCAGACAGAGATCCCCCTGTGAATACTGGCACGGGAACCTCAGAGTCCTGAAGTGGAATACATGTGCCACAGTAAATCATAGATCTATTCAAAGACTGAGACAAGGGGACATTGAGCGGACATGAATGAAAAGTGTGTTGGCCGTATTGGAACAGGGATCACTGGCCACCATGATTAACACGAGAGCGGCATCAGTCCAAGGCTGAGTGGACAGTTCCCGGGCAGATGTCCTTGTAAAAGTCCTTTGTGTATCCAAGGGGTGTCCTTTTAAGCGTCTGCACACTGGTGCCTCTGTCAGTCTTTCATGATGGCCACCACTTCAGACATGTTCATCTTATGTGTGCCAATAATCAATAGCAAGGTAGATCCTTTAGGGGTCCGCTTCACTCCATCTAATGTACCTCAGTCCTTCCTTCCTCCTCTTTCATTTCCTCCCGGCTGGCACAAGCTGTGGGGGGGGGGGGGGCCCGCTACTCCACTGCAGCTCTCAAAGCCTGAGACTGGCCACTGACTGGATCCTCTCCCCCTCAG
Seq C2 exon
ATCCACTCTCTCTGCTACAACGACTGCACCTTCTCCCGAAACACCCCCAGCAGGATTTTCAACTACAACTTCTCAGCTCTGGCAGGCACCGTCTCTCTGGCAGGGGTGCCGAGCTTCACCTCGAAGGGGCTGAAGTATTTTCATCATTTCACCCTGAGTCTCTGTGGAAACCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000040412-5330417C22Rik:NM_001033304:13
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:
PF076998=GCC2_GCC3=WD(100=45.5),PF075629=NCD3G=WD(100=30.7),PF076998=GCC2_GCC3=PU(80.4=46.6)
A:
NA
C2:
PF076998=GCC2_GCC3=PD(15.7=13.8)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CTGTGCCCTAGAAGCCTCTGA
R:
TCCACAGAGACTCAGGGTGAA
Band lengths:
346-2319
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: