MmuINT0108822 @ mm9
Intron Retention
Gene
ENSMUSG00000015579 | Nkx2-5
Description
NK2 transcription factor related, locus 5 (Drosophila) [Source:MGI Symbol;Acc:MGI:97350]
Coordinates
chr17:26975610-26978510:-
Coord C1 exon
chr17:26977970-26978510
Coord A exon
chr17:26976593-26977969
Coord C2 exon
chr17:26975610-26976592
Length
1377 bp
Sequences
Splice sites
5' ss Seq
AAGGTAAGG
5' ss Score
10.51
3' ss Seq
CTGCCTCTCTTCCCCTTCAGAGC
3' ss Score
12.42
Exon sequences
Seq C1 exon
CCCAATGGCAGGCTGAATCCCCCCTACTCCAGCCTGCTCCCGCCTCTTCTGCCCCTGGTGCTCCGCGCTACCTGCTGCCGCGCGCCACATCCAGGGCAGAGAGGCGGGTGCGCGGGCGGGCGGCGGGCACCATGCGGGGAGGCTGTCCCCAGGGGTGGGCAGCACCACTCTCTGCTACCCACCTGGCGCTGTGAAACCTGCGTCGCCACCATGTTCCCCAGCCCTGCGCTCACACCCACGCCTTTCTCAGTCAAAGACATCCTGAACCTGGAGCAGCAGCAGCGTAGCCTGGCGTCTGGGGACCTGTCTGCGCGCCTCGAGGCCACCCTGGCCCCTGCCTCCTGCATGCTGGCCGCCTTCAAGCCCGAGGCCTACTCTGGCCCCGAGGCGGCAGCGTCCGGCCTGGCAGAGCTGCGCGCGGAGATGGGCCCCGCGCCTTCGCCCCCCAAGTGCTCTCCTGCTTTCCCAGCCGCCCCCACATTTTACCCGGGAGCCTACGGTGACCCTGACCCAGCCAAAGACCCTCGGGCGGATAAAAAAG
Seq A exon
GTAAGGAGAACCTCAAGCTCTTCCCTTCTGGAATCGCTTTCATGTCCAAAACCCTGAGCCAAGAAACCCAGGCCTGACAGTAGCTCAGTCCGGGGTGAAGGCTGGGCGCGGGGAGTTTGGAGTATAAGATTCCAGGCTGTCCCGCAGTCAGTCCGAAGTTTAGAGGGAACGCCGAATTTAGAGGGTCAGGAAAAAAGAAGGGAGAGAGAGAGAGGGAGAGAGTGAGAGAGTGAGAGTGAGAGAGAGAGAGAGAGAGAGAGAGAAGATTAAAATGTTGTTTTCGGCCTACAAAACCCCAGTAGGTTAGGGCCTTGTTCTTGGATCTGTTACAAAGTTAAGCTATCTAACAATCCGCGTTAGAACAAATCTTCGTACTGGAGAGTTAAAATCTCTTCCAGATTTGGGGGTACTTTGAGACACTGAGAACTGCTAAACCGAAAGCTTAGCCCCGTGTATCCTGGGCCTTGTGTAGCCCACCCTGCCTTTCTGGGCCTTGCCTCCTTTGTGCCAAAAGAGAGGAGTCTGGGGACCGGGTTGTGATTTTGAGATGCGATGCTGCGGATCCCAGGAGCTGGGGTTGGCTTTGTTTTTCTAGTACAATCTCCAGGCAGGATCAGGCAGAAATTCCTTTCTGGGAACTGTTGGGAAATACGGAACGAATAAAGACACTGAGAAGTGAAGAGCAGGCTTCCGAAGGTGGCCGAATACCAAATATCTCAGAGTAGGGAGAGGGGCTCCTGGCCAGCTCACAGAAGGAGCAGGGAAGTCCCAGGCCCAGATCCTGTGCTGAGTAAAGCCAGAGAGGCCCAATGGTTTCTGCGAGTTAGAGGACGTTCCTAGGTTTTCCCTGGGAGCAGAGAGAAGGTCCAGGAACATTGGAGAAGGACTGGAGGAGGATTAGAACTTATTGCTACCAACCGGAATCCCGCAGGGCTGGTGTAGAGGCCTCTGTCCTCCTCCGGGTACTGGGAAGTCCAGAAGCCATGCCAACATCAGCTGACCACCCGAGGGACAAACCGGAGTATTCCTAATGTAATTCACTCCGAGCATCCTCATGACTTTATTTTCTTTGCAGCCAGAAAAGCTAAAGCTAAATCCCAGACTGTTAAGAGAACGCTAACTATCCGGGGAAGAGGTCTGGGATAGGGCGCCCGAGATTTCTCTTGTTTTGTTTTGTCCAAGCCACTTAGGCATTTCCCAGATGCGCAATTGCGCCAACATCGAACCGAGCGAGCCCGTGCACTCGGCGATTAGCTTAAGCGGAGCTGGGTGTCCGGCATAGGACCAGAGTGATACTCCCTGCCACCCCTACAAGGGCCCTGAGGTCCCCGGCCCGCCGCTCTAACCCGCCACCTCTCTGCCTCTCTTCCCCTTCAG
Seq C2 exon
AGCTGTGCGCGCTGCAGAAGGCAGTGGAGCTGGACAAAGCCGAGACGGATGGCGCCGAGAGACCACGCGCACGGCGGCGACGGAAGCCACGCGTGCTCTTCTCGCAGGCGCAGGTCTACGAGCTGGAGCGGCGCTTCAAGCAACAGCGGTACCTGTCGGCGCCAGAGCGCGACCAGCTGGCCAGCGTGCTGAAGCTCACGTCCACGCAGGTCAAGATCTGGTTCCAGAACCGTCGCTACAAGTGCAAGCGACAGCGGCAGGACCAGACTCTGGAGCTTCTGGGGCCGCCGCCGCCGCCCGCGCGCAGGATCGCGGTGCCCGTGCTGGTGCGCGACGGGAAGCCCTGCCTGGGGGACCCCGCGGCCTACGCTCCCGCCTACGGCGTGGGTCTCAATGCCTATGGCTACAACGCCTACCCCTACCCCAGCTACGGCGGCGCGGCCTGCAGTCCCGGCTACAGCTGCGCCGCCTACCCCGCTGCGCCCCCCGCCGCGCAGCCCCCCGCCGCCTCCGCCAACAGCAACTTCGTGAACTTTGGCGTCGGGGACTTGAACACCGTGCAGAGTCCCGGGATGCCGCAGGGCAATTCGGGCGTCTCCACGCTGCACGGCATCCGAGCCTGGTAGGGAAAGAGCCCGTTTGGGGCGCCCCGGAACGACTCCCACCTTTAGGAGAAGGGCGATGACTCCGGGGATGGGAAAGCTCCCACTATGCCCTGTCCCTCAGATTTCACACCCACCCTCGCGCAGGCCTGGGACCTTTCTCCGATCCATCCCACTTTATTGACGTAGCCTGGTGTCTCGGACCTGGCAGAGCCCTTCCAGGGTCACGGGCACTTTCGACGGATTCCACACTAGGACCGGGAGCCTGGGCCGGGCGCCCGGGCCCTGGTTGTCTTGCCGTCGCCCACCCACCCGTATTTATGTTTTTACCTGTTGTAAGAAATGAGAACCCTCTTCCCATTAAAGTGAGTGCGCTAACGC
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000015579-Nkx2-5:NM_008700:1
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.595 A=NA C2=0.221
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0004624=Homeobox=WD(100=27.3)
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:
CAAGTGCTCTCCTGCTTTCCC
R:
TTGCACTTGTAGCGACGGTTC
Band lengths:
342-1719
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: