MmuINT0006125 @ mm9
Intron Retention
Gene
ENSMUSG00000056004 | 9330182L06Rik
Description
RIKEN cDNA 9330182L06 gene [Source:MGI Symbol;Acc:MGI:2443264]
Coordinates
chr5:9440720-9441807:+
Coord C1 exon
chr5:9440720-9440983
Coord A exon
chr5:9440984-9441633
Coord C2 exon
chr5:9441634-9441807
Length
650 bp
Sequences
Splice sites
5' ss Seq
CAGGTAAGG
5' ss Score
11.08
3' ss Seq
TTCTCTGTCTTTAAATGAAGGAC
3' ss Score
6.44
Exon sequences
Seq C1 exon
AACAGACGATTCATCAATGATGTGGTGAAGATTTATTCTATCACAGCCACTAATGCAGTTGATGGGGTAGCAGCGTCATGTCGTGCCTGTGCCCTGGGCTCTGAGCAGTCGGCCTCATCATGTGTACCCTGCCCCCCAGGCCACTACATTGAGAAGGAAACCAACCAGTGCAAGGAGTGTCCAGCTGACACCTACCTGTCCATCCACCAGGTCTATGGCAAGGAAGCTTGCATTCCGTGTGGGCCTGGAAGTAAAAGCACCCAG
Seq A exon
GTAAGGACGTGGCTGTCCAGTTACTCCCTCTGGGGTGGTGGAGGCAGAGGTGGTGGAGTTGCTATCGATGCTGGAAAATGCTCTGCAATTCTCATTCCTGTTTTCTCTTCTCTTACATTAATTGAGCTCTGAATTTATGCTGTGGAAATGCTGGTTACTAGTCACAAAATATGAGGGAAAATATTTAATAAGAAGTTTTTCAAAAATACTACAATTGATATCTTGTGCATTTCCAAGATAGGAGGAGCTGTCCTGTGAGCTGGGTGTAGGAGTGCCTGGGGAAGCAATACTCGTGGTGTACAGCATTTCAAGTTTGAAGCAAATCAGCAAGCCAGCAGATCAGAGTAGCTTAACGCAAATGTTTTATTGTCTGTGAAAGCAGGCCTCATGGAAAGATTTTAGTATTTCTTAAAAATAGCTTCCCATAAGGAGGTTATCTGAGAAAATATCCCTGATTAAAAAAATCTTGACTCTTCTGCACTTTTTATAGAGACATTTAGCAATTAGGAATCCTCTATCCCTGGTATAACAAAATATAACTAAGACAAAAATTACTGGAAGATTTTATAGCTAGAACTTTTGAAAACATTTTCTTCATAGTAGTTATTAACTTTCTGCATTATTGTTTGTTTCTCTGTCTTTAAATGAAG
Seq C2 exon
GACCACTCGCTTTGCTATAGCGACTGCTTTTTCTACCATGAAAAAGAAAACCAGACTCTGCACTATGACTTCCGCAACCTCAGCAGTGTAGGCTCGCTGATGAATGGCCCCAGCTTCACCTCCAAGGGAACGAAATACTTCCATTTCTTCAATATCAGTTTATGTGGACATGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000056004-9330182L06Rik:NM_172706:14
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.008 A=NA C2=0.000
Domain overlap (PFAM):
C1:
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
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
ATGCAGTTGATGGGGTAGCAG
R:
GTTCCCTTGGAGGTGAAGCTG
Band lengths:
343-993
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: