MmuINT0074702 @ mm10
Intron Retention
Gene
ENSMUSG00000053129 | Gsx1
Description
GS homeobox 1 [Source:MGI Symbol;Acc:MGI:95842]
Coordinates
chr5:147188696-147190947:+
Coord C1 exon
chr5:147188696-147189298
Coord A exon
chr5:147189299-147189777
Coord C2 exon
chr5:147189778-147190947
Length
479 bp
Sequences
Splice sites
5' ss Seq
TGGGTAAGC
5' ss Score
8.84
3' ss Seq
CCCCCCCCATCGCCCTCCAGACA
3' ss Score
9.13
Exon sequences
Seq C1 exon
CCAGCACCTCGCCCGCTCCGGGAGGTGCCCGCAGCAGCAGCCAAGGTGATTCCAGCCCGGGCTTGAGCCGCGCGTGGAGCCTCCGGGGCCCGGGAAGCTGCGGGTGGCCGCGGCCAGGGGAAGCTACGACAGGATCTGCAGTTCCCTCGGGCTCCAGGGGCGGGCTGGCGGCAGGTGGACCGCGCGCCGGAGCCATGCCGCGCTCCTTCCTGGTGGATTCCCTTGTGCTGCGGGAAGCCAGCGACAAGAAGGCTCCGGAGGGCAGCCCGCCACCGCTCTTCCCCTACGCGGTCCCGCCGCCGCACGCGCTCCACGGCCTCTCGCCGGGCGCCTGCCACGCGCGCAAGGCCGGCTTGCTGTGCGTGTGTCCCCTCTGTGTCACCGCTTCGCAGCTGCACGGGCCCCCCGGGCCGCCGGCACTGCCGCTACTCAAGGCGTCCTTCCCTCCCTTCGGATCGCAGTACTGCCACGCACCCCTGGGCCGCCAGCACTCCGTGTCCCCTGGAGTCGCCCACGGCCCGGCTGCGGCCGCAGCAGCTGCTGCACTCTACCAGACCTCCTACCCGCTGCCGGATCCCAGACAGTTTCACTGCATCTCTGTGG
Seq A exon
GTAAGCGGGGTCCCCGCGCGAAATTGGGGGGCGGTGGTCCCGGGGTGGGGGGAAGTGAGTGAGCTAGGGATGGGGAAACGGCGCGCTATGGGGGACGGTGAGGATACTCGAGGGGCGCTCACAGTGCTAGACTGGGACCGGACGTAGGAACCGGGGAGAAGCCAGAAAGATCCTGGGGCGAAGGGGAAGGGGTTAAGGCCAGCTTTGAGATGTTCCTTAAAGGGGTGTTAGGGACAACCGATTCCGAGGAGAATTGGAGTCTGTGACTTGGCAAGGAGGCACCCGCCTGTGGAGTGATGAATGGAAGGATGGAAGGGATGTGTGCCTGATTCCAAGGTTGAGGCTAGCCTCAGTTCAGCGGGAAATTAGGCCCAAGGCTCAGAGGTTTGATGATCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTTTCCCTCCCTCCCCCCCCCCCCCATCGCCCTCCAG
Seq C2 exon
ACAGCAGCTCGAACCAGCTGCCCAGCAGCAAGAGGATGCGGACGGCGTTCACCAGCACACAGCTCCTGGAGCTGGAGCGAGAGTTCGCCTCCAACATGTACCTCTCCCGCCTGCGGCGCATCGAGATCGCGACCTATCTGAACCTGTCCGAGAAGCAGGTGAAGATCTGGTTTCAGAACCGCCGGGTGAAGCACAAGAAAGAAGGCAAAGGCAGTAACCACCGCGGCGGAGCTGGGGCGGGGGCCGGCGGGGGCGCACCGCAAGGCTGCAAGTGCTCTTCGCTCTCCTCAGCCAAATGCTCAGAGGACGACGACGAATTGCCCATGTCTCCATCTTCCTCCGGGAAGGATGACAGAGATCTCACAGTCACTCCGTAGGTGCGCCTTTTAGAGGACCATTGGTTTCCCCACCCCCCACCCCGACCCTTCCCGCACTGGTCCCCAGGCACCCGCTGGCCAACCGACGGATTTCGTTGGGCTTTGCGGTGGTGCGCAGCTTTAGGCAGAGCTAAGACCTTAGCAGACACTTGAAGACAGTGCCCCTGTCCCTTGGGCTTCAGGGTGTTTAGGAGGACTCCAAGCGATGAAGGCTGAGTCCTCCTCCTAGGACACAGCCTCTTCTCCCAGGCACGCAGGCCGGAGCACAGCGCCTTGCTGACCGCCAGCGCCTCTTCGCCTGCCAACTCTGGGCTGGTTCAAGCTTCCTCGGTTCCACTATTCTCTCCTTCTCGGTCAATCTGGGCTTTTCACTCCGCGAGTGGCTGTTTGCTTTTCTTTTAACATTTCTTTCTTGCCCCCAACTCGTCTCCCCCCACTGTGGTCCTTTATGCAACACGTCTATGGACTTAACTTTTCCTTCCCTCCTCAGGAAGTCTCTCCCTTCTGTCCGTTTGTCCCTTAAACAGGGATCAGGTCTTGCTGTTCGAAGAAGTCCCCCTAGCAGAGAGAACTGTCTCACATGGTATTGTATTGGGGAAAATGACTCTGTTTCCAATACGCTCTAAACCCCCTTCAAATGAAGCCGCTGTAACCAACCTCTCCCCATTGTCCAGGCCCCGACTCCCTCTGGGGACTGACTGACTGTGTCATTGTATCGTCTCTGTAATGCCAGAAGATATTTATTTATTTATTTATGTACAAAATTTTAAATAAACTTTTTTTTTCTTAGAAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000053129:ENSMUST00000065382:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.153 A=NA C2=0.456
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0004624=Homeobox=WD(100=45.2)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping 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:
TACTCAAGGCGTCCTTCCCTC
R:
TCTTCACCTGCTTCTCGGACA
Band lengths:
342-821
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