MmuINT0068491 @ mm10
Intron Retention
Gene
ENSMUSG00000029275 | Gfi1
Description
growth factor independent 1 [Source:MGI Symbol;Acc:MGI:103170]
Coordinates
chr5:107721376-107723408:-
Coord C1 exon
chr5:107723223-107723408
Coord A exon
chr5:107721864-107723222
Coord C2 exon
chr5:107721376-107721863
Length
1359 bp
Sequences
Splice sites
5' ss Seq
CAGGTAAGC
5' ss Score
9.88
3' ss Seq
GGCCTCCTGTGCCTTCACAGCGT
3' ss Score
8.87
Exon sequences
Seq C1 exon
AGGGCGGCGCTGTGAGTGCAGGCGAGTCGAAAATGGAGCCCCGAGAGCGTTTGTCCCCCGACTCTCAGCTTACCGAGGCTCCCGACAGGGCCTCCGCGTCCCCCAACAGCTGCGAAGGCAGCGTTTGTGACCCCTGCTCCGAGTTCGAGGACTTTTGGAGGCCCCCTTCTCCCTCCGTGTCTCCAG
Seq A exon
GTAAGCCTTGATTCGAGGTCTTGTGGCAGAGTTCTGGAGTCGCAGCACGGAGGGAAGCCCGCACAAGGGATGCAGAGGGTCGGCCTAGGGATCTGGCTCCTAAGGGAACAGGGTTCAGGGGAGGCATCCAGCTTTTGTGCTGGACACCTTGCCCAAAGTGTCCTCTGCCTCCTTCTAAGTCCCTTAGCTCCAGGCTGGCCCTTAATTCGTTTGCCTGGAACTAACAGGCGAGGTCAAACGAACTGGTCCTTCTCTGGCTGGCATTTCTTTTATGTCCAGAATTCATTGTTTAGAAATTGTCAGATCCCAGAATCCAGGACCCAGACCTGAATACTTCAAACAAGAGACCTGGGCAGTCTGAGCGGTACAGAGCTGGGCACCACACTGGAGTGCAAGGCTGCTGCTGAAAATCTCAGCTCGCTGGCTCTGTCTTCAAAAGTTTCATTTTCTCCCCTTCTGCTAAGAGGGCCCAGGCAGGGGCACCAGCATGCTCGGGCTCATTTCCAGGGAGCAATTGACTAGAGTTGATGGGGGTGGGGTGGGGGTGGGGTGGGGGTGGAGGTGGGGGGGGATATCTCGGGTCACAGCAGAAGTAGAAAGGAGACCAATCCAAATTCTACTAAGAGCAGGCTATTTCCCTTTCACACTATTAGCTCATTCACCCCCACAAGCAGAGGGTTGGTTCTTCCTAGCTGTGTGACCAAGCTGCTATGGGACAGGTCCGCCCAGAATGGAGTGTGCATTTACTTGCATTCATTCAATATCCAATTTTAGCAAAATTCACGTGTGTGAAGGGAGAGGAGTTCTTCTGAAGGTAGTGTAATTTTTAACTGTAATTTTTCATCAGAAATTTATCAGGGATGGGCATACTTCGCGCCCTTGTCTGCTGCCCCTTGCGTCATAGCTTTGAGAAATCTTGGGGACATTCCAGTTTGTTTAGTCTGATACTCCTAGATAACCTGGACTCAACGTGGATCGGCCTTCTCCGTTCTTCCTAATCTATTGCAAAGAGAAAGGAATTGAGTAGAGGAGTACTTGAAAGGAGTCAGGACCCTAGACCTAAGTTCTCCTGTCTGTCTCAATCTTTCTAGCAGGTTCTGGGGACTGGGGGTGGGTGGGGTCCAGCCAGAGAACCATCAAAACGAATTTACCCACCTCTTCAACCTGTATCATTTTAAGTATCACTTTACTGCTCTGTCACTGGTCCTGGAAGCCCCGCGGGCCTACCTGAGTTTCACCCCGGGTGTCGGGGGTACTTGGCTTTCTAATCAGCTAGGGCGCCTGACAATAGTGATGGTGCACTGCGGGCTCCGCCCAGCAGCCTCGAACTTGACTCAATGGCCTCCTGTGCCTTCACAG
Seq C2 exon
CGTCGGAGAAGTCACTGTGCCGCTCTCTGGACGAAGCCCAGCCCTACACGCTGCCTTTCAAGCCCTATGCATGGAGCGGTCTTGCTGGGTCTGACCTGCGGCACCTGGTGCAGAGCTATCGGCAGTGCAGCGCGCTGGAGCGCAGCGCGGGCCTGAGCCTCTTCTGCGAGCGCGGCTCGGAGCCGGGCCGCCCGGCAGCGCGCTACGGCCCCGAGCAGGCTGCGGGCGGAGCCGGTGCGGGACAGCCAGGGAGCTGCGGGGTCGCCGGGGGCGCCACCAGCGCTGCGGGCCTGGGGCTCTACGGCGACTTCGCGCCTGCGGCGGCCGGGCTGTACGAGCGGCCGAGCACAGCAGCAGGCCGGCTGTACCAAGATCATGGCCACGAGCTGCACGCGGACAAGAGCGTGGGCGTCAAGGTGGAGTCGGAGCTGCTTTGCACCCGTCTGCTGCTGGGCGGCGGCTCCTACAAATGCATCAAATGCAGCAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000029275:ENSMUST00000159164:3
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.676 A=NA C2=0.165
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GAGTGCAGGCGAGTCGAAAAT
R:
GCTCGCAGAAGAGGCTCAG
Band lengths:
344-1703
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development
- Ribosome-engaged transcriptomes of neuronal types
- Neural differentiation time course
- Muscular differentiation time course
- Spermatogenesis cell types
- Reprogramming of fibroblasts to iPSCs
- Hematopoietic precursors and cell types