MmuINT0006355 @ mm9
Intron Retention
Gene
ENSMUSG00000043419 | A030009H04Rik
Description
RIKEN cDNA A030009H04 gene [Source:MGI Symbol;Acc:MGI:1915359]
Coordinates
chr11:69154271-69156149:+
Coord C1 exon
chr11:69154271-69154560
Coord A exon
chr11:69154561-69154660
Coord C2 exon
chr11:69154661-69156149
Length
100 bp
Sequences
Splice sites
5' ss Seq
ATGGTGAGG
5' ss Score
7.61
3' ss Seq
ACCCTTCTTCTTTCCTCCAGTGC
3' ss Score
11.04
Exon sequences
Seq C1 exon
GTGCCCGTTCTGCCGCGCGCCTTCCCCGCTCCCGCGCGGCGGCGTCACGGAGATCGCGCTAGACCCTGTCTTGTGGTCACGGCTGGAGGAAAAAGCCCGGGCTGAGCGTGAAGGAGACCCGATGGGGAGCCCGGCCAAAGACAGCGGAGAGGATGGAGAGGACGACGACGGGGAAGCGGAGAGCGAGAAGGGGGCGGGACCTCCAAGTGCGGGTTGGCGCGCGCTTCGCCGAATTTTGGACAGGGTCCTGGCGCCGGCACGCCGCTTGCGGCGTCCGTTGCCTAGCAATG
Seq A exon
GTGAGGGGCGGCCTAGGGAGGATACTGGGTACATTGCACCGAAGAATGCTGGGTCAAGTTGCATCCTCCTGTTGCCACTAACCCTTCTTCTTTCCTCCAG
Seq C2 exon
TGCTCTACTGTCCAGAGGTCAAGGACATTGCCCACATGACCCGTTGTACGCTGTAACCAAGGAACCCCAGAGCTATGGCAGAAAGCAGGTGGGAGCAGCATCCTCAGGCGTGCTCTGACACAAAAGGTTGATGTCAAGACTACCTGGAAATCAAGGCTGATGCTGGAATTGGTACATGCGTGATGGAGATGGAGCTCAACAGAAAGGACCCTAGATGGTGTGGATTCTGAGCGGCGAAGGCTCCTAGACTGTGCCAGCATTATATTTTCAGGATGGAGTGGCCAAGGGATAATAGAAACAAAGCCTACCATAATGTAGGAAGAAAAAAAAAATAACAAAGCTTTGGCGTTTGTTCAGAGTCTGTGGTGTAAGCAAAGGATCCAATTTTAGCAGTGGTCTGTGGTTGACAATGTGTACTGTGGAAAAAAGGACAGGACAGGGGATAAGCTAATTTATATGTCATGTCAATCTCACTTATCTGGTTGTGTTTGCTGGCATGCCATCTTCCCACTCTTGTTACCGTGCTCCAGCAATTACTGAGTTGACTCCCTGCTTATGATTGGGAATCTTGCATATACAACCTCCCTTCAGCTGGATAGGGCAGGTATGAAAACATCCAAGGGGCATTTATTTACATGAGGCCTTATTAAAGGCTTATCAAAGATGGGTGAGCCATTTGATAAAGGAAGCAAAATTTAGGCCTTTGTTATCTTTACTGACTCTGTAGCAATACTGGGGAAAAGAAAAAAAAAGATGCTCACATAATTTTAATTTGTGTCCCATAATGGGACATTGTTTACTGTATGTAGTTAGTTCTATTCTAAAGTCCTGTAAATATCTTACTGTAGACTTAAAATCAAGACCAGCAGTGTTGGTTGGTCTCACAGCTTGCTAGAAATGCAGAATTTCAGGACCCCAGTCCACATTCCCCGGTAGTTTTAGAATCCCAGGTATGTGTATGTAAGTTAAGAATCACTGGTTTAGCTCTTAGTCACTCTGAGATGGCATCATCAGCTGTAGGTGGAACATTTAAAACACTAGTGACGCATTAAAGTGCCAAAGTGACATTCTTTTGAGAAAAATTTTTCTGAGCTACAAATGTGAATTTACAAGGCCTCAGTTTTCAGAGGTCTTCAAGATTTTGTTTTTAATGACAAATAATGTATGTAGTTCTAGGGTATAAACCTCCATTTGTAAAATGTTTTGTCTTTTTCCTGTCCTTCGGTTCCAGCTGAAATCTCCCCTTTTGGAGGCCAGCATGCATCTGTGGGAATGTGTATGTTTTCTCTATACGTGTTGCCAAAGGGAATGCTATGTTTATTTTCTGCTATTTTATGTTTTGAGTATTTCTAGAGTATAAATTTCAAGTGACTATCTCCAGAGCCGATAGCAGTGTTAATGTTATATGTATTCAAAAAAAAATGTTTGCTGAATTTATTTTGAATGTAATAGTCTCTAGAATAAAGTATCTGGGCTCATTCAATCTGTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000043419-A030009H04Rik:NR_027827:1
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
NonCoding
No structure available
Features
Disorder rate (Iupred):
C1=NA A=NA C2=NA
Domain overlap (PFAM):
C1:
NA
A:
NA
C2:
NA
Main Inclusion Isoform:
NA
Main Skipping 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:
AAAGACAGCGGAGAGGATGGA
R:
CCCACCTGCTTTCTGCCATAG
Band lengths:
247-347
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: