MmuINT0164883 @ mm9
Intron Retention
Gene
ENSMUSG00000064043 | Trerf1
Description
transcriptional regulating factor 1 [Source:MGI Symbol;Acc:MGI:2442086]
Coordinates
chr17:47460227-47461603:+
Coord C1 exon
chr17:47460227-47460611
Coord A exon
chr17:47460612-47461536
Coord C2 exon
chr17:47461537-47461603
Length
925 bp
Sequences
Splice sites
5' ss Seq
CCAGTGAGT
5' ss Score
8.28
3' ss Seq
CTCTAGCATTTGTGTTTCAGGCA
3' ss Score
6.08
Exon sequences
Seq C1 exon
GAAATCCCCCGGAAACATCCACCTATCGCCGCCAAAGTTGAGGAGCCCCTCAAGAACCTACCAGAGAAGAAGAAATTCCGGCACCGGCCTGAGCCCCTCTTCATCCCACCACCGCCTTCGTCCTATACTCCCAACCCCACCTCTTACTCGGGGGCCACCCTGTACCAGAGCCAGCTGCGCTCCCCGCGAATCCTCGGGGACCACCTGCTCCTGGACCCCGCCCACGAACTGCCCCCCTACACGCCGCCACCCATGCTGAGCCCTGTGCGCCAGGGCTCAGGGCTCTTCAGCAATGTCCTCATCTCTGGCCACGGCCCTGGAGTGCACCCCCAGCTGCCCCTCACTCCCCTCACGCCCACGCCACGTGTGCTGCTGTGCCGTTCCA
Seq A exon
GTGAGTCGTCCCTTAACCCCTGGTGTCAACCTCTGTCGATTTGAATACTACCCTGAGTGGGTGGGGAGTCACACTTTCTTCACCTGGCTAGTTTACCCCGCGGATTTCTGTGAAATACCCATTATGTGTACCACATTCGATGCGAGGTGGTCTTAAAGACTCCGCATCATCGCATTTAGTAACTCGAGGGAAGCAGTGTGAGGAGAGAAGCGAGTCAGAGAGAGTGTCTTTGGGATAAAGAAAACGGGAAATGTGCACTCTAAGACTGCTTTGGATGGTCAAAAAAGATGCTTAAGATAAATATTTAGCCGTTATACACATGGCAGCTATTACTAGCAAGAGTAAATCTTAATATTTACTGTGCTTTAAAAAAAATCCATCATGAACCCTGTAGGCCATATGTGAGTGTAGCCCCAACTACTATAGAAACTGAGGCAGAAGGGATTGGGGGGGGGGTTGAGGGCCAGCCTGAGCAGCACAGGAAAACCCCATCTCCTCCGTAGATATTGAGGGGGCCAAAGGGAGATGAGAGATCTTTGTAGCTAGGTTTCTTTCTGGTTGCCTAGAAACCATGTAGCTTAGCCAGCCAGCTTTAACTCACAGTGTGAGAAATGGCTATCCTAAGGCCTGTAATCCTAAGCACTGTGGAGGCTGAGGCTTAAGGCTGGAGGATAGGAAGTTCAAAACCAGATTGAGCTACACATCAAGACCCTGTCAAGGGGCTGAAGGATAGGGAGAGAGAGAGAGACAGAAAGAAAAAGAACCTCATGAATCCATCATATCTTCTGGAAATTGATATGAATTGGGTAGGAGGAGAGCTTTGTTATTTTTGGCTAATCACTGATCAGCTAACTTCAATCTGTATTCATTTCTTGGGATTTTTTTTTTTCTTGTTGTCTGGTAAACTCTAGCATTTGTGTTTCAG
Seq C2 exon
GCAGCATCGATGGCAGCAATGTGACAGTCACCCCAGGACCTGGAGAGCAGACTGTGGATGTTGAACC
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000064043-Trerf1:NM_172622:7
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.744 A=NA C2=0.739
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
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CTGAGCCCCTCTTCATCCCA
R:
ACATCCACAGTCTGCTCTCCA
Band lengths:
358-1283
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: