MmuINT0108820 @ mm10
Intron Retention
Gene
ENSMUSG00000044220 | Nkx2-3
Description
NK2 homeobox 3 [Source:MGI Symbol;Acc:MGI:97348]
Coordinates
chr19:43612325-43615892:+
Coord C1 exon
chr19:43612325-43612849
Coord A exon
chr19:43612850-43614305
Coord C2 exon
chr19:43614306-43615892
Length
1456 bp
Sequences
Splice sites
5' ss Seq
AAAGTGAGT
5' ss Score
8.4
3' ss Seq
ATGTCTTGCTTCTCCCTTAGAAA
3' ss Score
8.95
Exon sequences
Seq C1 exon
CAAAACCCAGACCCCCAGGTCCCGGCCAATGGAGGGGATTTAGACTGGACCGCGTCTGTCAAAAGCTCGACTCCGCACCACCGCGGAGTCCAGAAGAAGAGCTGGAGCCACCGCACTCCCTCCCCGCCCCCGCCGGGATTTATTGAGTATTTGGACTGGACAATTAAGTGGCCCTGATGATGTTACCAAGCCCGGTCACCTCCACCCCTTTCTCAGTCAAAGACATTTTGAATCTGGAGCAGCAGCGGCACTTCCACGGAGCTCACTTGCAGGCGGAATTGGAGCAGCACTTCCACTCGGCACCCTGCATGCTGGCCACGGCTGAAGGGACGCAGTTTTCCGATGCAGGGGAGGAGGACGAGGAAGAAGAGGGAGAGAAACTGTCCTATTTGAACTCACTAGCTGCTGCCGAGGGCCATGGAGATTCGGGTCTCTGTCCTCAGAGCTATGTCCATACAGTTCTCCGAGACGCTTGCAGCGGGCCCAAGGAACAAGAAGAGGAGGTTGTGAGCGAACGGAGCCAAA
Seq A exon
GTGAGTAGAGGGGGAAGGAAACGCGTCCGCACACCTGGGGCAATGGCTCAGCGCCTATAAACCCACAAACCGTGCCTGCATGGCCACCCGCCCCTTTCACATTCGGCTAGGGTCATGCCTATGCCAGGTTCAAGGACAGCTCTGCAAAGCACAGGTACCTGAGATGGTGCTGGGGCGGGGATAAAAGAGAAAGAGAGAACAGCTCTTGCCCGGAGCAGGGACCCGGAGCAGTCCCCGAGGGAAGGAAAAGTGATTATTGCAATCCTGGTTCCTTGAGTAATGAGTGACGGGGGCCCAGAGCCTGGGTCGTAACTTGTCCGTTGTGTGTGTGTTCTCTCGCACACCCATCTTCTCAAAAAAAAAGGGGGGGGTCAGTTTTCTGCCATTTTTCTGTCTTTCTTCTAACGTGAGGTGAATTCAGCGAGGCCAGGGCAGTCACCCCGGCTGTCCCGAAAAGGCAGTGCAAGAATGTTGTGTTTGGGCCATCCTTTCGGGCAAGACTTTGAGAGACACCAGCTTACTTCGGAGCTTGCAGTTCTTACGTTCGAACTGCAAGGAGGAGAGGTGGTGGCCAATGTGTGGGAGCTCGATCCATATCAGATGACGGCAGCAAGTCACACCCAGGAGGTGAAGGCCTCTGAAAAAAAATATCGTAATGCTCGCTTTGTTTCTTATACTGCAGGCGGAGTGGAATGGTTAAAGTTCCTGAATTAGTTCTGAGTGGGATTCTGGCCATTCAGCAGATCAGAGGTGGGGCAGGCAGGAGAATCAGATAATTGAATAAGCCCATAAGGAAATGTCTGAAAGGGAAACAGGATCAAATAATCTCTTCTCCGAGTGGAGATTTGATCTGGCTGAGACCAAAATCTTTTCTCTAACAATTCTCCAGGCCTAACACAGACATGAAACTGTCTAAATCGGTCCATCCAACTGTTTTTCCTCTGTAAGGTAACATACAGATACTGTCACAGACGCGTTCTCAGTAGTTTTGAAAATTAAAAAAAAAATCAATTCTTGAGCTGCACATACGCCTTTCACTTAGATATTTCCAAAGAGAAACAATTTTTGCAATCAACCCATGCATCCAGGCCTCCAGTCCCCAATACCAACTCGTTCCACACCTTCAGGGGAGTGGAAGGCAAACGAGTTTGCAGATACGGGGTCCTGTTCCGCGGTCGCCTGAAAATTGTTATTAGCCCCTGGACCGGCACATTTAATCTATTTTCTCGCTGATGCTCAAATTTAATAAATGCGAGCTAATTACTCTCACCGAATACGCCTTCTCCCGGTGGAGGTGCTCCGCCTGACGCGGGGGGGATGGGGGGGGCGGAATTGGGCTCCAGAAACTATGAACTTTCCCCAAAACTAGCATTTACTACGGGAGTGTTTTGTGCCTCTGGGGCGCAGGGGTGGTATCCTGAGAACTAGAAAGGCTAATGTCTTGCTTCTCCCTTAG
Seq C2 exon
AAAGCTGTCAGTTGAAGAAGTCTCTGGAAGCGGCGGGAGACTGTAAGACGAGCGAGGACGGCGAGAGGCCGAAGCCGCGGAGCCGCCGGAAGCCCCGGGTGCTCTTCTCGCAAGCTCAGGTCTTTGAGCTGGAGCGCAGGTTCAAGCAGCAGCGGTACCTGTCGGCGCCCGAGCGCGAGCATCTCGCCAGCAGCCTGAAGCTCACGTCCACGCAGGTGAAAATCTGGTTCCAGAATCGCAGGTACAAGTGCAAGAGACAGCGGCAGGATAAGTCCCTGGAGCTGGGGACGCACGCGCCGCCGCCGCCACCCCGCCGCGTGGCAGTGCCGGTGCTCGTGCGGGACGGCAAGCCGTGCGTCACGCCCAGCGCACAAACCTACGGCTCGCCCTACGGCGTGGGCGCCGGCGCCTACTCCTACAACAGCTTCCCCGCCTACGGCTACGGGAACTCGGCCGCCGCAGCCGCTGCAGCCGCCGCAGCCGCAGCAGCAGCGGCGGCTTACAGCGGCAGCTACGGCTGCGCCTATCCGACCGGTGGCGGCGGTGGTGGTGGCGGCACGGCCTCCGCGGCGACCACCGCCATGCAACCCGCCTGCAGCGCCACCGGCGGTGGATCCTTTGTGAACGTGAGCAACCTGGGAGGCTTCGGCAGCGGCGGCGGCGCGCAACCCTTGCATCAAGGTGCTGCAGCCGGGTCCGCGTGCACGCAGGGGACTTTGCAGGGCATCAGGGCTTGGTAAGGCCTGGGCGGGACACGCGGCGGGCGTCCTACTGCACGCTGGGCACCGCGGGAATGAGACACGAGAAAGGACAGACCCAAGGGCCAGGTCCCCTCGTTAAAATAAAAATACAGACGTATCGCTCCTTCCAAGGGGCCATGGTCGCAGCTCACTCCAGGCCTGGGGCATGGAACTCAGCGGAGAAAGGATGCCCTGGTCCAGTCCTCAAGACTGAGACAGAAACACCGGCCAGGCGCCAGGGAAGAGGTGGCCTCCCATCCTGACTCTGCGGAGAGTGCGGGAGGCTGGGACTCCGGCTGTCGCTTGCTCTCCGGAGGAGGAGGAGGGCTTTTCTCTTCCTGCTTTCCCTTGGCCTTCTCCGAGTGTGGTCCGGGAACCGGACCGAACAAGGGGGGAGGGGGGAGAAAGAAAGAAAGAAAGAAAAAGAACAATTTAAAGAAAAAGAAAGGTAGTTGGAGAGAGAACGTGAAGGAGAGGAAAATGGGGTACTAGCTTGAGAAATTCCACCGATCCGCAGCCCCTTTTGCTTGCCCGGAGCGCCACAACGAAGTGGATTTTTCCTTTTCCAACTGTGTCCCTTCCAAGACAGACTCCGCCCGGATCCCTAGATTGTCAGGGGACTGTTCTTGGAGACCACCACCGCAGTGAGATCGAAAGTTGGGGGAAGGGAGGCAGCTGAGCAAATCCAAGACCTGTCCGCCCAACCTAGGTTGTCGCCAGGTTGGTTTCCTTTCTGTTTTGTATTCTGTATTCCGCACATTATCTCTCTATAACTATATCCACACGCCGTGTACACAGCCGCTGTCACACACTACAGGAGTCAATAAAGAAGGTGCAATATTTCTGA
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000044220:ENSMUST00000057178:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.530 A=NA C2=0.211
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0004624=Homeobox=WD(100=23.1)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CCATACAGTTCTCCGAGACGC
R:
ACTTATCCTGCCGCTGTCTCT
Band lengths:
347-1803
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