MmuINT0068491 @ mm9
Intron Retention
Gene
ENSMUSG00000029275 | Gfi1
Description
growth factor independent 1 [Source:MGI Symbol;Acc:MGI:103170]
Coordinates
chr5:108150395-108152428:-
Coord C1 exon
chr5:108152243-108152428
Coord A exon
chr5:108150884-108152242
Coord C2 exon
chr5:108150395-108150883
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
CGTCGGAGAAGTCACTGTGCCGCTCTCTGGACGAAGCCCAGCCCTACACGCTGCCTTTCAAGCCCTATGCATGGAGCGGTCTTGCTGGGTCTGACCTGCGGCACCTGGTGCAGAGCTATCGGCAGTGCAGCGCGCTGGAGCGCAGCGCGGGCCTGAGCCTCTTCTGCGAGCGCGGCTCGGAGCCGGGCCGCCCGGCAGCGCGCTACGGCCCCGAGCAGGCTGCGGGCGGAGCCGGTGCGGGACAGCCAGGGAGACTGCGGGGTCGCCGGGGGCGCCACCAGCGCTGCGGGCCTGGGGCTCTACGGCGACTTCGCGCCTGCGGCGGCCGGGCTGTACGAGCGGCCGAGCACAGCAGCAGGCCGGCTGTACCAAGATCATGGCCACGAGCTGCACGCGGACAAGAGCGTGGGCGTCAAGGTGGAGTCGGAGCTGCTTTGCACCCGTCTGCTGCTGGGCGGCGGCTCCTACAAATGCATCAAATGCAGCAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000029275-Gfi1:NM_010278:2
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
NonCoding
No structure available
Features
Disorder rate (Iupred):
C1=NA A=NA C2=NA
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
- Muscular differentiation time course
- Spermatogenesis cell types
- Reprogramming of fibroblasts to iPSCs
- Hematopoietic precursors and cell types
Other AS DBs: