MmuINT0164877 @ mm9
Intron Retention
Gene
ENSMUSG00000064043 | Trerf1
Description
transcriptional regulating factor 1 [Source:MGI Symbol;Acc:MGI:2442086]
Coordinates
chr17:47485599-47490894:+
Coord C1 exon
chr17:47485599-47485805
Coord A exon
chr17:47485806-47490681
Coord C2 exon
chr17:47490682-47490894
Length
4876 bp
Sequences
Splice sites
5' ss Seq
GCTGTAAGT
5' ss Score
8.56
3' ss Seq
TCGCTCCCTTTCTTCCTCAGGTG
3' ss Score
11.8
Exon sequences
Seq C1 exon
ACCAGCGAAGAGGAAGAGGAGGCCGAGGAGGAAGAAGAGGACCCAGAAGAAGATAGGAAATCCATAAAAGAAGAGGAGAGTGAAGTGGCCAAGTCTCCAGAGCCACCGCCTGCCCCTGCCCTGGCTCCCACTGAGGGGCCACCCATGCAGGCTGTTGGCCAACAACCATCAGGCAACTTCATTTGTGAAATGCCCAACTGTGGGGCT
Seq A exon
GTAAGTATCTGTGTTGTCCCTGGCTCTGAGAGACGTGAGGGTCATACAGCTGTGCCTAGTTCTAAGAGCAGTGGACTTCTGGCAGATGCCTGCCACGTAGCTACCACTTTCTTACTCGCTTGGCCGAGGGAGAGTGGCTGTATGTCCTCTGCCAAGTGTGATACTGCATGCTGGGGAATTGAGGAGGGCCCTAAAGCCAAGCCAAGCATGGCGGCACAGGCCTGTCATGCTCAGCACTCTGGGGGCCGTGGTAGGGGAATTGAGACCTTGAGGCCAGCCTGTGGTACATAGTGAGACTTTGCCTCCAGGAGGTATGCTGTGCATGAGAGCAGGCCTCCAGAAGGCACACACTGTCTACTATACTGTCTCCTGGTACTCTGCAGGTCCTCAGACTGTGTGGCACCCAAGGCCAGATTATACCTTGTCAACATGCATTTAAATTCACTAGAAGATTCCACCAGGGTTCCCCTTTTATAACACAGTGACTTGCCTGAAACCGCCTCCAGTTTTATCTCTCTGGAAGGTTTAACTTTTCATATCCTATGAAAGTGTTACTACTTCTAATTCAAATGTCACATAATTGACATCTGAGCAAGTTGTTTCCAAGCAACTAAAGTTTGACTCGGCAGCCTGAGGGGACAAAACTTCACTAAGCAACTTTATGATGTGACCAGGATGAGGGAGAGTCTGGGAGACCCCTCTGCCTCCTCCTGAGCCCAGAAGAGCCTGTTGTGATGTGGTGACTAAGCCAGCTCAGTCAGTCAACAGGTTCTCCAGGGCAGGAGTGAGGACTGAAAAGACAGAAGACAATTAGACAACACTGTGACATGACCCCAGCCAGTTCTGAGGCTGAAGCAGGTTTATGGGTTTTTTTCCAGCCTGCTTTTATATCACTTTAAGTACGTGCAAAATAATAAGATCAGTTCTGGGTCAGGGAACAAGCAAGACAATAAACAAAATCCCCCGTAAACACCTTTCTAGGGACTAGTCAGGATGTGCAAGACAAAAGGAATGCCACACACAGCCTCAGCTGAGCCTGCTCTGAGCTTTGCATTAGTTCAAATGCAAATGCTCTTAATCTGGGCCTATTTCCTGAGTCCAGATTCCCGCCTTGACCTTACTTCTTTAGTCCTGGTCAGATGTCAAATTGCTGCCAAGAAATTTCAAGAAGTGGCCCCCCAAAGCACTCTACATCTTCCCCTTTTTTATTTCAGAAACAAGACTATGCCTGTCTTAGGTCATTCTAACAAGAGAGCCTTCCTTACCTGTCATAGAATATGCATTATCAAAAGCAATGCTATTCTGACTTAGGTTAGTAAGGCTCTGTGCAGAATCTTACTTGTCATTGGCTGCCAACCTGTTAAATTAATAACTGTCTGGGGATCCATTTTTAGTTTCAAGACATGTATTGTGTGGCCACCAACATAATGATGTTGTTAAAGGCAAGTTTTATCACAATGGGCAGGAATAAAAGTATTCCCAGGACAAGAAGTGCTAGCATGATCAAGCTATATATGCCATTCTTGAAGCTTGGCCAAGATACAAATACTGACCTCAGGCCACAAATAATTTTATCAGCGATATCTGGAGCATTAAAACTCAGCAGAGTAGCATCCTTTAAATTCATAATCTCACTATTCAAAGTTAAAACATCCAGAGAGGTGTTAGAACTGTGCCAAATACCCAGCAAGTGTCTTTGAACTTTTTCCCAATTATAGTGACAATCATTGTAAATTTTAGAAGTAACACAAATCCATTGGTATTTAGCATGACACTCGAGGTGGCTCCTTACTCTTAAACTCTGAGCCTCCTCTCTAATAGTTTGAATAGTATCATAAAGAGCATCAATCCTTTGTTCCAAACACCTGTCTAAATCCTCTTGAATATTCAGATCATTAGTAACATTTTTTGCTAAATAATTAACAAAAGTAGCTGTCTTAACTTCTTGTGACAAAGCAATTGCAAAAGCAGTGGTGCTAGCTATAAATGTAATCAAAGCTGCTATACCAGCAACAATCAAGCCCACTACCCTCTTGCTTCTGCTTAAAGCCTGATTCACTTATTCCAGTACCTGAAGTTTTTTGTTTTTTTTTTTTCAGAATACTAAGGTCCTGTCATACTCACAGGTTATAAAACAAAAGCTGGTTGATAGACCACCATAACAGACATGTCAGACTGCAATACGCTAAAGCAATTAGAAAATGTTCAATCAATATAACTTACATTAAATACTGCAGAAGAGACAAAAATAGTTTTAAACATGGCCTATTAATAAAATATTAGGAGCTTTAACACATGCACTAACACTTGTTCAAAATCCAGATCCTATTCCAGTTTTATCCACTGCAAATGTAACTTCATACAAGGCAGTTGTGAATTTTCAAATGTCTCTGAAAATGCCCAGAACCAGCCTTCTAAATGAAGACAATTATTTCAAATTCAATATTCAATATTGAATTGATTTCTAGACCAGTCCATGATAGAGTCAGAACAACATTAAAGGAAGTAGAAGAGGCACTATAACAACTTCTCTATTTGATTAATTTTTTCAAAGGCAGTCTCAATGTTCTCTGTCCCACAAGGTCTAAAAGCTTGAGGCAGGGCAGCTTGTCCAGTCAGGGATATAGGCAAGCAAAGGTGGGTCAGGAACATATTTCCAATATAGCTTCCCTGTCACCATTGTCAGTATTGCATTCAGCAAGCTCACACGTCAGCATCATTCTTCGTCCCAGCATCAGCATGTCTCACCAATCACCCTGGCAGCCACCAGTGCTCTTGTAGCCAGTGTCCTCTAAGGCTCCACACCCCAGAGGCTGTGTAGCATGGCTTCTGTGTGTCCTGCCTGTCCCCACTAGTCTTCACTCCTGACATTTCCCCACATAGGGTTTCCTAAAGCCTGACACACTGGCATAGACACGTTCTAGAGGTGTCACCCGCTTCTCAGGAAGCTCCATCGTCTTCCAGCTCATCCTTGCTTGTCTGATACAGAGCATATTGATGCTGTCATTGAGTCTGCCATTTAAAGAAAGACTGTAAAGTGTTTATATCCTGGGCTGGGCAGGTGGCACACACCTTTAGTCCCAGCCCTCTGAAGGCAAAAGCAGACTTCTCTAGTTCAAGGCCAGCCAGGACTACCTAGTGATACCCTGTGTCAAAAGAAAGAAAGAAGTAAAATGTTTTATAAAATGTTTCCAGAAAAATGAAATAAAATAAAATAAAAATAATAGAAGTGATCCAGTTGGTGATAACACATGTCTTTAATCCCAGCACTTACTTGGGAGGCAAAGGCAGCTTGAGTTCACAAGGCCAGCCTGGTCTACAGAATGAGTTCTAGGACAGCCAGGGCTATACAGAGAAACCCTGTCTCAAAAACAAACAAACATTAAATAGAAGTGCATGCCTGTTGCATTGCCTCTGTAAGGACATGGGAATGGCCAGCCTGCTGGGTCTCTGGCAGCCTGGCCTCTGCATCCCAGCACTGGATTTTGTTCAAAAGGCTTCCTGCAGACTAAGATGTGACTTTAAATGACAATGTTTCTTGGTGAATTTGTTCAGAAACCGGGTGCTTTTTCAATTCATTCTTTAGGGTACAATAAATGTTTGGTTTTTAATTTGGGGGATTGGGGTTCATTTTTTATTTGATTTCTTTTTTTTTGCAGAGGACGGGAGTCATCTTTTACTTTGTCCAATCAGACATGCTCAGCAAGATAGACGTTCTTAGTGACTTTTTAAAAATCTCATCAAAGAGCATGTGATTGATGGTTTATTCCATGCCTAGCAGTGAAGACTGGGTTCAGTAAATCAGAAATAGATTTTTTTTGTAATATAATAAAAAGGACCCGTGAGCTAAACAAAGAGAGGCCACCTAAAGCCACTGTGGTGGAATAAAGTCTGTTGGTTTGGAAGGCTGTGGGCCATAGCCCAGTACTCCAGTGGCTCTGGACAGAGGATAATTTGGTCCTGCAAGAACATTTTTGCTAGGACTGGGAAGGTGGGGCCGGCATCTGGTGGGTAGAGGCCACAGAGGCCTCTAATCACCTGCCGTGCACAGGACAGTCATCACCTGTCCAGTCCCATGTATCCACAGGGCTGAAGCCAAGAAGCCCAGCTCTGTAGAAATATTTGAAAAGCCAGCCAGGCATAATGGCAGACCTGTACTCCTAGCACTTGGAGGAGGAAGGCTGCTATACAGTAAGGTGAAGGCCAGCCTGGTCTGCAGATTAGACTCTAACTCAAAGAAGTCATTGGTCTGCGAATTTCCAGCCAGGCCTAGTGATAGAGACTTGTAATTCTAGCACTCAGGAGATAGGCAGGAGAACTGCCTCATGTTTGAAACCATGTTTTAAACTACAAGAAAGCCTGGCTCTTTTGGCTTCCGTGGTGCACTTGGGTTGCAGATGTAGCTCAGAGCAAGAACATTCATCTAGCAAGCTTGAGGCCCAAGTTCTGTCCCTAGCATCACAGAAAGCAATGAGCTACTGAGGGGTCCTCTAACTCCTCGTTTTGCACTTAGAGAAAAAAATAAAATAAAAAAAGAAGTATTTGAGAATTGAGTGGTTTAACGGCCTCTGATATTTGCACCCAAGTTTCAAGTTAGAGCTGGATGCTAAAAGTCTCCTGGCTTTGAGTTAAGAGCTTTGTCCTTGGTACTAAGCCACGTGGCCTTGCACTCTGGTTAGACCAGGGGAAGGAAGTTTTATCTGCACAGATTTCGTGGTTGGGGTATCTAAGCTTTGCTTTCTGTGGCACATGCCCAGTGCTTGCTTGTGTGAGCCCTGTGCTGTTTCGTGTATCCCGTGTTTTGCCACCAAGTAACTAACAACCCTAATTTCCTTTTCAGGACTGTAGATGTCATGTCGCTCCCTTTCTTCCTCAG
Seq C2 exon
GTGTTCAGCTCCCGACAGGCACTGAACGGTCACGCCCGCATCCACGGCGGCACCAACCAGGTGGCTAAGACCCGAGGTGCCATCCCCTCTGGGAAGCAGAAGCCAGGTGGCACCCAGAGTGGGTACTGCTCAGTGAAGAGTTCACCATCTCACAGTACCACCAGTGGAGAGACGGACCCCACCACCCATCTTCCCCTGCAAGGAGTGTGGCAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000064043-Trerf1:NM_172622:14
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.841 A=NA C2=0.831
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
No suggested primer sequences
R:
No suggested primer sequences
Band lengths:
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: