MmuINT0164882 @ mm9
Intron Retention
Gene
ENSMUSG00000064043 | Trerf1
Description
transcriptional regulating factor 1 [Source:MGI Symbol;Acc:MGI:2442086]
Coordinates
chr17:47454717-47456567:+
Coord C1 exon
chr17:47454717-47454870
Coord A exon
chr17:47454871-47456300
Coord C2 exon
chr17:47456301-47456567
Length
1430 bp
Sequences
Splice sites
5' ss Seq
CAGGTCAGC
5' ss Score
7.16
3' ss Seq
AGCCTTTATTGTCTATGTAGGAG
3' ss Score
6.33
Exon sequences
Seq C1 exon
CAGCGGCCAAACCAAAGGAGTGTTTGGGGAACAGTTTGATGCCAAGAACAAGCTGACATGCTCCATCTGCCTGAAGGAGTTCAAAAGCCTGCCCGCCCTGAACGGCCACATGCGGTCCCACGGGGGGATGAGGGCGTCCCCCAGCCTCAAACAG
Seq A exon
GTCAGCAGGGAGCCCGCTCCGTCCTTTCCGGGCCATGTGCTGCTTGCTTTGCTTTGCTGCTGATGGAGTGAGACAGGGGAACGTGTGCCTTCTGTGGGCACCAGGAGAGGCACAGTCTCCCCTTCCCTGGCTTCTTAGACAAGTGTCGAAAGCGCAGTGCTAGAAATCTCTTTAGAGAATCCTATTCCAGAGAAAGGTGCTGAAAGGAACTATGTCAATGTGGGATCTATAAATATGTAAATGCCAAGTATATACACATGCAAGTGTAAAGTAGAATTGAAATCTAAAGTATATGGAAAGTACTTGAGACCATAACCACACGGTCTCGGAGATCGGGGGGTCAGTGTAGGTAGAATCCAGTGATCCTGTAATACCCTCAGGATTATCCAGGTGGACAGTCATGTAAGAAACCATCTTTAGGTTTGGTTAAAACTCAGGATTTTCTGGAATTTTCTTTGAGTATTGAATTTATGAGTCACTCTCCCGACTCTATTTCCTGGCTATGCCAGATAAAAGAGGAGTTTATCTCCCCTTTTTTTAAAAAATTATTTTATGTGCATTGGTGTTTTTGCCTGTATGCATGTCTACGTGAGGGTGTCAAGTCACTTGTATGACATAGTTCTGAGTTGCCATGTGGGTACTGGGAATTGAACTTGGATCTTCTGGAAGTGCAGCCTGTGCTTTTAACCATCTCTCCAGCCTGTCTTCACATTTTAAAAACAGAACGTTGGCAGGTGACTCATGGCTCATGCCTCTATAATCCCAGTGCTCGGGAGCTAGGGACAGGGGGATCACTCCAAGTTGAGACTAGCCTGGTTTACATGGCATGTTCAAGGCTTGCTAAAGCAACATAGCAAGACCCTTGTCTCAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACCAGAACAGAAAAATGTATGTTTTCAGCCTGTTGTGGCATTATACACCTGTAAACCCAGCAGCACTCAGGAGGCTGAGGCAGGAGGATTCTGAGTTTGGGCTACCTTTTGAGAATCTGTCTGAAAGAAACAAATATAACCATAGCATATTTTGCATTTTCAATGGGGTTTCCTGACCTCAATAAAATTTAGGCTGAAATGATTGTTTCCATTAGACACAGAGTCAACTGAGACCCAAGAAATGGAAATCTACATAAAAATCACGTTTAGTTTTGACTGAATAGCAATCCCTTTCCTTTGCTTCAAAAAGCCACGAAAGCCACCAACTTCTTTTTTAAAAAAAAAATTTTTTTCATATACAAGTGATATCTTAAATGTAGCTCAGGGACCCAGAGTTACAGGAAGGAAACCACCCAGCTGTGGTTTTCTGCTCCCCACCACTGATGTCCTGGAACCTCTGAGGAAAAGCAAGTCCATCTCCCTTGGGAGAGCTGCTTTCAGCCCAGGATCAAAGCCTTTATTGTCTATGTAG
Seq C2 exon
GAGGAAGGAGAGAAGGCCCCACCGCCTCAGCCTCAGCCCCAGCCTCAGCCCCAGCAGCCACTGCCACCTCCGCCTCCTCCGCCGCCGCCACCGCAGCTCCCTCCTGAGGCAGAGCGCCTCACGCCTATGGTCATGCCCGTGTCTGTCCCTGTCAAGCTAATCCCACCCAAGCCCAGCTCTCAGGGGTTCACCAACAGCGTCGCTGCCACCCCCGCGGCCAGAGACAAGCCAGCCAGCTCGATGTCGGACGACGAGATGCCTGTGCTC
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000064043-Trerf1:NM_172622:5
Average complexity
IR-C
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.673 A=NA C2=1.000
Domain overlap (PFAM):
C1:
PF139121=zf-C2H2_6=WD(100=46.2)
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CATGCTCCATCTGCCTGAAGG
R:
ATCTCGTCGTCCGACATCGAG
Band lengths:
355-1785
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: