MmuINT0164880 @ mm9
Intron Retention
Gene
ENSMUSG00000064043 | Trerf1
Description
transcriptional regulating factor 1 [Source:MGI Symbol;Acc:MGI:2442086]
Coordinates
chr17:47450742-47453609:+
Coord C1 exon
chr17:47450742-47452449
Coord A exon
chr17:47452450-47453562
Coord C2 exon
chr17:47453563-47453609
Length
1113 bp
Sequences
Splice sites
5' ss Seq
CAGGTATCT
5' ss Score
7.33
3' ss Seq
CCTATTTGGCTCAAAATTAGATG
3' ss Score
2.45
Exon sequences
Seq C1 exon
GTGTGAAGGACTTTCCCCCACCACGGTGGTGTCTGGTCCGTACCTCCGCCCGGGTGAGGATGTAGGCACCTCGGCTCTGCTGATGACCTGTTCAAGCCAACAGGGACCCCTGTCTCCAGCCACCCTCACAGACATGTCAGCCGTGGAGTAGGGTGGACGCTTTCTCTCATCTTCTCAGGGTTTCAGGATTTTTCTTCTTTCTTTTTTTCTTTTTTTTTTTCTTGGTTTTTGGTTTTTGTTTTGTGGCTGAACACTCATAAGCAAAGAGGACATCATGGGGGACCAGCAACTGTACAAGACCAATCACGTGGGCCACGGTGGTGAGAACCTCTTCTATCAACAGCCACCCCTTGGTGTCCACAGTGGGCTGGGCCACAGCTATGGGAATACAATCTCTGGGGCTGGGATGGACGCCCCGCAGGCCTCACCCATCTCGCCTCACTTCCCTCAAGATACTCGGGATGGTCTCGGCTTGCCTATTGGCTCCAAAAACCTTGGCCAGATGGATACCTCCAGGCAGGGAGGATGGGGAAGCCATGCAGGGCCTGGGAACCACGTCCAGCTTCGTAGCAACTTGGCCAACTCAAACATGATGTGGGGGACGCCCACCCAGGTGGAGCCCGCTGATGGCTACCAATACACTTATTCCCAGGCCAGCGAGATCCGGACCCAGAAACTCACCAGTGGTGTTTTGCACAAGCTGGACTCTTTCACCCAGGTATTTGCCAACCAAAACCTGCGGATTCAGGTCAACAATATGGCCCAGGTGCTGCACACCCAATCAGCGGTGATGGATGGAGCCTCCGACAGTGCCCTCCGTCAACTGCTGTCTCAGAAGCCCGTGGAGCCCTCAGCATCAGCTATAGCTTCCCGCTACCAGCAGGTGCCCCAGCAGCCTCACCCTGGCTTCACGGGTGGACTGCCCAAACCAGCCCTTCCAGTCGGGCAGCACGCTCCCCAAGGGCACCTGTATTATGACTACCAGCAGCCCCTGGCCCAGATGTCCATGCAAGGAGGACAGCCACTGCAAGCCCCTCAGGTGCTGTCCGGCCATATGCAACAATTGCAGCAGCACCAGTATTACCCACAGCCGCCGCCTCAGCAGCAGCAAGCCGGACTGCAGCGGATCTCTGTGCAGGAGATGCAGCAGCAGCAGCAGCCGCAGCAAATTCGCCCCTCACCACCTCAGCAGCAGCAGCAGCTCCAGCTGCAGCAGCGGCAGAGTTCACTGCAGATACCTCAGTATTATCAGCCCCAACCCATGATGCAACACTTGCAAGAGCAGCAGCAGCCATCCATGCACCTGCAGCCACCCTCATACCACAGGGACCCTCATCAGTATACCCCGGAGCAGGCACACGCTGTCCAGCTGATCCAGCTGGGCTCTATGCCCCAGTATTACTATCAGGAGCCTCAACAGGCCTATAGCCACCCCCTCTACCCGCAGAGCCACCTGTCCCAGCACCAGCAGCGTGAAGACGGTCAGCTGAAGACATATTCTAGTGACAGACAGACCCCGGCTATGCTGAGCTCCCATGGGGACATGGGAACTTCTGATACAGGAGTGGCAGATCCAGCCAGCTCAGAAATGACTCGGGTCACTAGTACTCTTCCTCACCAACCGCTCCTGTCCCCCAGTGGGATCCACCTCAACAACATGGGGTCTCAGCATCAACAGCCGCCATCTCCCAGTGCGATGTGGCCCCAG
Seq A exon
GTATCTCAGAGTTTCTCCCCATATCCACATGTGCGCCAGACTCAGCCAGGCGGGCAGTCTCTGTGGTGCCCAATTCTGCCTCCAACCTTCATCCTTTATGTTCTTTATACATTTCACAAAGGTTAACCTACATGTGCCAGGCACTGTCTGTGACAGACACTTGGAATACAAAATCAATTTGGATTCAGGCTTTGGCCTTGGGGATTTGTCACCTCACTAAAGAGATGACCAGAATATTTTAGTACGTCTGAAACGGTTAATGTAATGATCAGGACCTAGAATCACAGTTCAATCATGGGATGCAGGGCAGAGCTTGGCAGCAGGAGCTCGAAATCCCAGCACTGGGGAGGCAGAGACCAAAGGATAGATGGATGGATGGATAGATAGATAGATAGATAGATAGATAGATAGATAGATAGATAGATAGATAGATAAAAATGTTGATGTGGACATTGCCTGGGAAACAGTAGCCAAGGCTAGCCTAACCTCTAGCCTTCACTCACATGCCCACATGTGCATATAGAACCACATGCACTTGCACACATACAAACACATACACAGCATGTACAGTGTCTATGTCAGAGGCAAGAGGACCACAGAGTGGGGACATCTCATCCCCTCTGAAACTCTGTCCTTGCAATATCCCCAAGGCACAGATTGTCCTATGACGTCTGCACAATCACTGTGCACGTGGATGCTCCCCGCCCTCGACCCACACCACTTCTACACGAGCCATACATGCAGTCACACCTACGAAGTTCTTGTTTGCTTAGCTTTGATGCTATCAGGTCTCTTGGAATGATGCGGTACCACTCACTTCCTGTCTGTCCTCTGTGGGGATGGACCCTGTTAGTGCAGACTTGATACAGACTTCTTAAGAAGGGTAGAAGGGCTGGCGTCATCTGAGTTCAGGGAGCAGTGGGAAGAAACCAGATGTGGAACAAAGGCATGTCAGGGTAATCGTGGGCAGAGAAAGTTCTGGAAGGGTAGATCCTGGTGTTCGTACAACTTGAAATTCCTCACTTTAAAAATACATGTTTGTTTGTTTGTTTGTTTGTTTGTTTTTTTCTCTCTTCTTGTTTTCTTCCGGTGCCCTATTTGGCTCAAAATTAG
Seq C2 exon
ATGCACTTACCTGATGGGAGAGCCCAGTCCGGATCCCCGGAATCAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000064043-Trerf1:NM_172622:3
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.860 A=NA C2=1.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
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:
GCCCCAGTATTACTATCAGGAGC
R:
GCTCTCCCATCAGGTAAGTGC
Band lengths:
342-1455
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: