MmuINT0074703 @ mm10
Intron Retention
Gene
ENSMUSG00000035946 | Gsx2
Description
GS homeobox 2 [Source:MGI Symbol;Acc:MGI:95843]
Coordinates
chr5:75075601-75077893:+
Coord C1 exon
chr5:75075601-75076337
Coord A exon
chr5:75076338-75076965
Coord C2 exon
chr5:75076966-75077893
Length
628 bp
Sequences
Splice sites
5' ss Seq
TGGGTAGGG
5' ss Score
4.66
3' ss Seq
GCTCTCTTTTGGGTCCACAGGAG
3' ss Score
8.46
Exon sequences
Seq C1 exon
GAGGACCAACCCTCTCCAGGGACCCCTTTGTTCGAGTCCCAGACACCTCAGCATCCCCAAGGACTTGACCGCCCGCGTGCGCCCAGCTTTCCGGACAGTGCTCAGATAGCAGAAGGAGAGAAGGGGACTCAGCAGCCCGCAGGACAAGCCATCCATCGACATGTCGCGCTCCTTCTACGTGGACTCACTCATCATCAAGGACTCCTCACGGCCCGCACCCTCGCTGCCGGAATCGCACCCAGGGCCGGATTTCTTCATCCCGCTGGGCATGCCGTCCCCGTTGGTGATGTCAGTGTCCGGGCCTGGCTGTCCGTCCCGCAAAAGCGGCGCTTTCTGCGTGTGCCCGCTTTGCGTCACCTCGCACCTGCACTCCTCTCGCCCGCCCGCAGGAGCTGGTGGCGGAGCTACGGGGACCGCGGGGGCTGCAGTGGCGGGCGGCGGGGTGGCTGGAGGCACCGGCGCTCTACCTTTGCTCAAAAGCCAGTTCTCTCCCGCTCCTGGGGACGCGCAGTTTTGCCCACGGGTGAGCCACGCACACCATCACCACCACCCACCACAGCATCATCATCACCATCACCAGCCCCAGCAGCCCGGCTCGGCTGCAGCGGCGGCCGCGGCGGCGGCGGCGGCAGCTGCGGCAGCGGCGGCTCTGGGACACCCGCAGCACCACGCACCTGTCTGCGCCGCCACTACCTACAACATGTCGGACCCACGGAGATTCCACTGCCTCTCCATGG
Seq A exon
GTAGGGCGGGGTACCTGCGTGCCTCCGGGGAAACAAACTTTGCGCCACCAGGGAAGGAGGTGGGAGTAAGGTGGGATCTTCTGTGGAACTGTTGAGATCTTCCCCTAGAAATTCCACGGAGGTGGAAGTTAAGGAGTCAACTTCTTGGCGAGGCCTTGTGCCCTTAGCTCTACAGGTGCACAAGTGTCGCCTGTTATCTGGGCTTTGGAGACCTGGATCAAGACTTCAGAGAAATAGGAGGTTAAACTGACTGAGATTTGGGGTGGATGCGTTTGGACCTCAGTGTGGCATCTTAGCTTCCCTGTTGGTTAAAGGCTGTCTGTGCCTTTGGCCGAGGCTGCTAGCTGGTTAGCTTTGCTAGGCCAATGGAAGACAGACAAGGGGAAGGAGAAGGCAGTAGGTGCAAGTTCCACTGGAGTCCTTTAACTTAAAATCCAGGACATTAAAGGCCTTAATTCTCATGAACGTCTGTCTTTCTTACACTCCCAGACAGACCAGGGACAAACATGGATGTGTTGGGTTAGACTGGGTTCTGGAGCCGCGTTCTTTCCAAGGGTTGTCAAGTAGAGTGGGGTCACTTTTTTTTTTCTGCGGTTCATCACCTCTCTGCTCTCTTTTGGGTCCACAG
Seq C2 exon
GAGGCTCCGATACCAGCCAGGTACCCAATGGCAAAAGGATGAGGACAGCGTTTACCAGCACGCAGCTCCTGGAGCTGGAGCGAGAATTCTCTTCCAATATGTACCTGTCCCGACTCCGGAGAATCGAGATCGCGACATACCTAAACCTGTCAGAGAAGCAGGTGAAAATCTGGTTTCAGAACCGTCGCGTGAAGCACAAGAAGGAGGGGAAAGGCGCTTCGAGGAACAATCACACAAGCTGCAAGTGCGTGGGTAGCCAGGCGCATTATGCGCGCTCCGAGGACGAGGACTCCTTGTCCCCTGCCTCGGCTAACGAAGACAAGGAGATTTCCCCCTTGTAAAGGCAGAGGCTCCTTCTGCTACCTGCTCCCGGTACCCTGCCCTCCTCCTCCCCATCAGCACAGGGACCAAAGTTCTAGTCCATTGCCCTCATTCCACCTGGAAAAGAAACTCTGAAAAGTCCGGGGAATTCAATGCCGGGCCCGACTTTGAAGCTAGCTCCTCTTTATCTGGGATTCCACTCAGTTACGGATTGGTTTTTTGTTTGCTTTTTTGTTGTTTTTAATGTAAATATCTAGAATTCTAACCAGTCTCATATATCAGGAAAAACCAGGGTTGATTAAAGTTTAACACTGTATGGGGGGAGGGGTTGGTTGAAGACGCATGCCATTTGCCCCCCTGTCTTTTCAGAACTTGATGAGAAGAGGGGTTTCTTTATTGTTTTTGTTGTTGTTTTAAAATGAAATCATTGAAGTTGCCATTAATATAGAGAGTTAAACTCCGTAGGTCTTGTTTTCTGAAAATTTTCATGGGGGAGAATTTTAAATCCAGGTCTCTGGAAGTCCCTTTGTATGTGAATAGTTTTATATAAAATACATATTTATATTTATTTAAATAAATGAAACGAAATAAATATTTTTTAATTCGT
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000035946:ENSMUST00000040477:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.518 A=NA C2=0.500
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0004624=Homeobox=WD(100=50.0)
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:
CACCCACCACAGCATCATCAT
R:
TCACCTGCTTCTCTGACAGGT
Band lengths:
355-983
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