MmuINT0112722 @ mm9
Intron Retention
Gene
ENSMUSG00000028256 | Odf2l
Description
outer dense fiber of sperm tails 2-like [Source:MGI Symbol;Acc:MGI:1098600]
Coordinates
chr3:144809727-144811580:+
Coord C1 exon
chr3:144809727-144809885
Coord A exon
chr3:144809886-144811494
Coord C2 exon
chr3:144811495-144811580
Length
1609 bp
Sequences
Splice sites
5' ss Seq
CAGGTGTCC
5' ss Score
3.16
3' ss Seq
TCTTTGAAAATTCCACTTAGGTT
3' ss Score
5.5
Exon sequences
Seq C1 exon
ATGAGAGGCCAGGTGGAGTCGAATCTGAAGCAGGTAGAGCAAGCCCGCAGCTCCTTCACGTCAGCCGAACAGAGACTTCAGGAGTGTCAGGAGAAGCTGCAGCGCTGCAAGGAGAAGTGTGCAGAGCAGGCGCTCACCATTAGGGAGCTTCAAGGCCAG
Seq A exon
GTGTCCATCAGCTCTGAGTCTTGGAAGATGTGTTAAAGAAACATTTGACGACGTCATTTCAGCAGTTGACGGCACGCGTGTCATCTATATCGCTGATGCAGTATTTCATGCAGATACTCGGCTGTTTATCTTTAGTATTTCCTGGTGACACTGGTCATAAAGATGGCTGATATGGGTGATTTATATGCATCTGCATTTGGACTTGGAGGACATAGTGTGGTGATGTAATGAGAGGAGGGCCAAGCCGGGCTTGCCTATCTGTTTCTTGACATCAGCATAAGACAAATAATAATTTACCTTGCAAAAATCAGAATGCATTTTAATTAGAATTGTGCATCACACTTATTGGGGTAATTCTATTCTTTCACTTAATACCTATCAGTCCATCCGCATAGGACTGTGTGACCTTGTCACCATACATCTCCCTCCTCCTCCCTCGGTGCGTGTCACAGAGCGCGCACACTTTGTACCTGCGTTAGGGCTACTTGGTGGTTTGTTGGAAGCGTGTCTGAGTCTGCAGGCCAGTCTGTTTCCTTACTTGTAAGACATCTCCAGGAAGAATTCACTTTGTGCCTTTCAAAAGAAACTTATTTAGCTTTTAAAAGACACAAAGCAAAATTCCAAGAAGAAATTCTACTAGAAAAAAACAATGCTACTTTAATAAGAATAAGAAAAGTTATTTTTTATGCTATGTGTGTGTGTGTTTTGCCTGCATTTCTGTGCACCACATGCATGTAGTGCCCAAAGTGGCCAGAAGAGGACATCATAGTCTGAGCTACCGTGTGGGTGTGGGGAATATAACCTGGGTCCTCTGGAAGAGAAGCCGGTGCTCACAACTGCTGAGCTATCTCTCTAGGCCTGAAGAGAAATATTCTTCTTATTAAAGCTACTTAAACTCTTTGAATCAGACTGTGAAGCAGTGGGAAGAATGGTCTGTTCTGACCTGAGCAACTTTGTCTTTGACTTTGACTCAGCATTGTCACAGGTAGTTCTCTATCAGTATTTTAAGTGGAGCATTGTTGATATGAGAAACATATCAATTAACATGGGAAACATAACAGATTAACTGTCTAATGAACAATGTTGAAATTTTTCACACACACATTTTTTAAGTTTTGTCTTGTTCTTGTTGGGGTTTTGTTTTGGAGGCAGGGTTTCATGTAGCCTGGACTGGCCTCAGTCTGAGGATAGACTTGAATTTCTAGTCCTCTTTCCTCTACTTCCTGAGCCAGGATTGCAGCACAAGCTTTCTGTAGTGCTGGGTTTGTACATGCTGGGAAAGTTGTTGCCAGCTGAGCCACATCCCTAGTCCCTGACAAGCTAAATGTTCCTTTTCATTAGAACCCTGTTCAGAGTATTTTAATTACCATCACCCAGGAAAAAATGTACTTCATTTTCTAACATAAACAACATCAGCTTTTAAAACTCTGTGAGGATCTGGAGAACTTGTAGATTAGCATTGTAAACATGGCTTGGTGTCTTTCTGTGTATTCATATCTTCTTGTTTCTTATACTTCTAAATAAAATACGTAATTTCCTTGGAAGTTGATGAAGAAAATAACTGAAAAAACCTGTCTTTTTCTTTTCTTTCTTTGAAAATTCCACTTAG
Seq C2 exon
GTTGATGGAAACCAAAGCCTTCTGACCAAGCTTTCTCTTGAGGAAGAAAATCATCTCATTCAGTTAAAGTGTGAGAACCTTAAAGA
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000028256-Odf2l:NM_001162538:13
Average complexity
IR-C
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.132 A=NA C2=0.034
Domain overlap (PFAM):
C1:
PF059116=DUF869=PU(3.6=11.3)
A:
NA
C2:
PF059116=DUF869=FE(11.2=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping 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:
ATGAGAGGCCAGGTGGAGTC
R:
AGGTTCTCACACTTTAACTGAATGA
Band lengths:
239-1848
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: