MmuINT0068490 @ mm10
Intron Retention
Gene
ENSMUSG00000029275 | Gfi1
Description
growth factor independent 1 [Source:MGI Symbol;Acc:MGI:103170]
Coordinates
chr5:107723223-107723886:-
Coord C1 exon
chr5:107723724-107723886
Coord A exon
chr5:107723409-107723723
Coord C2 exon
chr5:107723223-107723408
Length
315 bp
Sequences
Splice sites
5' ss Seq
CAGGTGCGA
5' ss Score
7.75
3' ss Seq
CTCCTGAATCTTTTCCGCAGAGG
3' ss Score
9.07
Exon sequences
Seq C1 exon
AACTCAGAGTATCCGAGGGTCCAAACATTCGTCCAGCGGCTGACCACCATGCCGCGCTCATTCCTGGTCAAGAGCAAGAAGGCGCACAGCTATCACCAGCCGCGTTCTCCGGGGCCGGACTACTCCCTGCGCCTGGAGACCGTGCCTGCGCCGGGCAGAGCAG
Seq A exon
GTGCGAAGCGCGCAGAGGCCGGGTAGGGCAGCTGCCGAGGACACCGACTCTGCTCCAAGCCACCTCGTTTCCTAGGAATCGGGGGAGGCTATCCTAACGCCCCTCGGGTGCTTTTTTGTTTTTGTTTTTGTTTCCCGGTGCTCAGATTTGCTGAGCTTGCCAGAGATGCCCCTGGCGCTCGCAGTCGGCTCTTGAATTCGGGAGGGAGGGCTCCCGGTTGGGTCAGAGTGGACAGAGGAGGACACGGGCGCCACGGTGGAACCACTTCAGTTCGGCCAGGTTTAGGTTTATTTCTCTCCTGAATCTTTTCCGCAG
Seq C2 exon
AGGGCGGCGCTGTGAGTGCAGGCGAGTCGAAAATGGAGCCCCGAGAGCGTTTGTCCCCCGACTCTCAGCTTACCGAGGCTCCCGACAGGGCCTCCGCGTCCCCCAACAGCTGCGAAGGCAGCGTTTGTGACCCCTGCTCCGAGTTCGAGGACTTTTGGAGGCCCCCTTCTCCCTCCGTGTCTCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000029275:ENSMUST00000159164:2
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.869 A=NA C2=0.676
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CTCAGAGTATCCGAGGGTCCA
R:
CTGGAGACACGGAGGGAGAAG
Band lengths:
347-662
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