MmuINT0006127 @ mm9
Intron Retention
Gene
ENSMUSG00000056004 | 9330182L06Rik
Description
RIKEN cDNA 9330182L06 gene [Source:MGI Symbol;Acc:MGI:2443264]
Coordinates
chr5:9445364-9446990:+
Coord C1 exon
chr5:9445364-9445553
Coord A exon
chr5:9445554-9446893
Coord C2 exon
chr5:9446894-9446990
Length
1340 bp
Sequences
Splice sites
5' ss Seq
TAGGTAAGT
5' ss Score
9.66
3' ss Seq
TGTTTTTCAATGTCATCTAGGTG
3' ss Score
8.85
Exon sequences
Seq C1 exon
GGGAGAAAGATGGCTCTCTGTACCAACAATATTTCAGACTTTACGGTAAAGGAAATGGTGACAGGGTCAGATGATTACACAAATTTGGTTGGAGCATTTGTATGCCAGTCAACTATTATTCCTTCTGAAAGTAAGGGCTTCCGGGCAGCCCTGTCGTCACAGTCTATCATTCTGGCAGATATGTTTTTAG
Seq A exon
GTAAGTCTCCTTTGGCTAATATATGTGTGTATGTGTTCATTCTCATTTTATCGTAACAATAACTTGTCATAATACTGTTGTTTACAACACACAAAGCCTGAAGTCTAATAAGCTGTCATTTTGCAAAGTAAAAATCACTATCAGCCAGTCTCAAGAGTTCTTCATTCCTGTGTGGAAATCTATGTGATAAAATGTTTTATGAGAGGCTCGCCTTCATTCGCATTCTTTAGTTGAATAGTTTAGATATAAAAATAGGCCTGGAGAGATGGCTCAAGGGTTTGTTGCCCAAGGGCTGGACCTGAGTTTGGAACCCTAGTGCCTTTGCAAAATCCGGGTGTGTGGATCAGCTTAAAATCCTAGTGCTGTTAGAGAAAGTCCCTGGGGCTTGATGGCCAGCTAGCTTAGCAGAAATGATTGATCTCTACGTCCAGTGAGACTCTGTTTCAAAGATAAGATAGAGATGGGAGATACCTCAAATCAACTCCATATGTATACACATGGCTGTATCTGTACAGATAAAAATAAAAATTCTTTATGAAAATCTAAAAAGCACGTAAGTTATAATATGGACTACTGAGTTTCACTGAGGATGCTGGTACCTTGGGTCTTGTTCCCTTTGTCTGAGGTCCTAAAGTATAGGAAAGTTTTAAAGTAACCCAGTTTCCTAGTGGTTCTTAGGAATCAAATTCATTATAACTGCTGGGAGCAGTGAAAATTTGGGGGTGTGAGACCTGATCTGAGAGTGTTGCTGTGGACTCCAAATGTACTGGGCTTCAAACTTCAGCACCAAGGTCAGCTGCCAGGTTCATGCTAATTGGCCGAGGTTTGCTGCTGCCACTGTTTTATCTAAGAGAAGGAAAATTCTGTCTTTCTGATTAAGCAAATCAGTAATTAAATAAAACTATATGAAGTATGGGCATGGGAGCACCAGGCTTGGTGAAATAAACATGTCTGTACTTAAGCTGAGCAAACATAACCTGTCTCTACTGACAAAACTCGGTGGAAGAGCACAATACTGGAATAGATTTTTGAAACATTAGAACTACAAGGAACTGTAGAAACCATCTAAACCACTGTATATATCCTACAGATTCTAGAAAAACAAAACAGAAGAACAAAACATCCTAGTGAAATGAGCTAGATTTCATGAAAGAATCTTTCTTTCTGGAGATGTTAGAAGATTTCTTACTCTTATCTGGAATGGCTCAGTTTAATATTTCTGGTGAGGGGATGGGTGAGGGGACAGTTGTCAAGGTAAAGCTATTTTGTACTCAGATGTACAGAGACTAAGTAAACCTAATCTTCCCTGCTGCTTCAGTTTGTTTTTCAATGTCATCTAG
Seq C2 exon
GTGTCACTGTTGACACTGCCTTGCAAAACGTTAATATCAAGGAGGATATGTTCCCAGTGTCACCGAGCCAAGTACCAGATGTTCATTTCTTTTATAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000056004-9330182L06Rik:NM_172706:16
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:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GGGAGAAAGATGGCTCTCTGT
R:
AGAAATGAACATCTGGTACTTGGCT
Band lengths:
280-1620
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: