MmuINT0078773 @ mm10
Intron Retention
Gene
ENSMUSG00000022485 | Hoxc5
Description
homeobox C5 [Source:MGI Symbol;Acc:MGI:96196]
Coordinates
chr15:103013815-103017429:+
Coord C1 exon
chr15:103013815-103014535
Coord A exon
chr15:103014536-103015227
Coord C2 exon
chr15:103015228-103017429
Length
692 bp
Sequences
Splice sites
5' ss Seq
ACGGTAAAC
5' ss Score
5.88
3' ss Seq
TGGGGGAATTTATGTTCCAGAGA
3' ss Score
4.79
Exon sequences
Seq C1 exon
GGGCTTTGCCAACATATCAAGATGCGTTTCGCCGGCTTCCATCACTAACCTCCCGGAGGTCATCAAGCCAAATTTATGAGTGGCCGCTCCAGTCACGTGACTCTATTTAAGGCTCCCTTATTTGGGAAGAGCGCATAGGATAAAGAAAGAGATATCTCCACCTATAAATTGTGCACTTTGGAGAACAAAAACCCCCTCAACTTCAAAGAGTCACAAATCACCCTTAATCAAAAAGGGTGCAGAAATTTTTTTTGGGCCCTCCCCGCCATGAGCTCCTACGTAGCCAATTCATTCTATAAGCAGAGCCCCAATATCCCTGCCTATAACATGCAAACTTGTGGGAACTATGGATCGGCCTCAGAGGTGCAGGCATCCAGGTACTGCTACGGCGGATTGGACTTAAGCATCACTTTCCCACCGCCTGCGCCTTCCAACTCTCTCCACGGGGTAGACATGGCTGCCAACCCCCGGGCTCACCCCGACCGCCCCGCCTGCAGCGCCGCGGCCGCTCCGGGACACGCTCTGGGCAGAGACGAAGCGGCTCCTCTGAACCCTGGGATGTACAGTCAGAAGGCGGCTCGCCCGGCGCTGGAGGAGCGAGCTAAGAGCAGTGGGGAGATCAAAGAGGAGCAGGCGCAGACAGGGCAGCCTGCCGGACTGAGCCAGCCACCGGCCCCGCCACAGATTTACCCGTGGATGACCAAACTGCACATGAGCCACG
Seq A exon
GTAAACTTTAGGACTTCATTTTGCGCGCTCGGGTCCGCCTGGGTTTTATAGGCCATGCGGGGCAAATAAAGAAAAAAAACCTGCGGCCATAAATTTTACGATCCAGGCATCAATGGCTCGTAAAACTGTCCACTAAAAGGCTTAGAGGCTGTGTGCGCCCAAATTTACGACGACATAATTGGATCATAGGAACAAAACGTGTATAAAAGGCAATATTCAATTTTGGGGGGAGAGGGAGGGAGTTAAAAAAATAGAGGGATCTGAAGGGTGAGGAGCATGGGGCTCCAGAGTGGGGATCCCCCCGCGGCTCCCTCCCTCCCTCCCCTGCGGAGCCGGCTCGGCCAGTGCTCGCGGCTCCGGAGGATTCCAGCGACTCGGGAGGGGCGGGAGGGGGGTCCCCGGTGCTCGGATCTCGAGGGTGCTTATTGTTCGGTCCGAGCCTGGGTCTCCCTCTTCCCCCCATCCCCCCTCAGCCCCTCCGGCCGCAGAGTGAAGGCGGCGGTGGAAAGTTTCCTGCCCAGGCGGAGGCGCTTCTCCCGGGACCGGGCCTGCCCGCCTGCGGCCCTTCTGGCCTGTCCCACCGCGCTCACCTCTACTCCCTCCGACCACGGGTGGGGCCTGGGACTAGGGTGGGACGTTGGAGTGCTGCACGCTATTCATCCCTCCCTGGTTTGGGGGAATTTATGTTCCAG
Seq C2 exon
AGACGGATGGCAAGCGGTCCCGAACCAGTTACACGCGCTACCAGACCCTGGAACTCGAGAAAGAATTCCATTTTAACCGCTACCTCACTCGCCGCAGGCGCATAGAGATTGCCAACAACTTGTGTCTCAACGAGAGACAGATCAAGATCTGGTTCCAGAACCGCAGGATGAAGTGGAAGAAAGATTCCAAAATGAAGAGCAAAGAAGCTCTTTAGAGGAAGCAGGGAGCCCTCAGAGAGCACCCCGGTCTGCTGTGGTCCCTGCGCCCTTCCTTTTCGGTTTTCCTCCTTCTAGATTTTGAGGCGGAGGCTAGAGCACTGGCTCCGGGCCTCCCAGACAAAAGCGCATTTCTTTGGCATTCCGAATCCCCATCGACCCAGGGTTCCGCAGGACCGCCTGCACTGCCTGTCTTGCCTCAGCTCAGCTGAGCACCCCAGGCCCGGGGCACATTCTTGTAGGGCGGGTACTGGATAAGTCTCAGCCTGGGCTGCCTCTCTCGGCTCCGAGCCCTAGTTCAGCTAGCCTGAGTTAAGGTGAGACAGACTGACTGTAACCCCTTCTCCCCGACCTCCGCCTCACCCTCTTCTTTGTTCCTGCCTAGGCTGACCAGCCTGCTGAAGGCTGGTTGTGCCAGGCAGAGGCTATGACTAGCTAGAATCGGGGTGCTTTCAACTAACCTTTGTAACTTCTAAACTGTCTTTGCTCATTAATTATTTGCATATGAAAGAGGGAGATAAGTGAAAGTGGGCCTGTAACCCCGGAGGTTGTCCTATGCTCTCTATACCTTCCAATCCCCTTCCCAAAGCCCGGGAACTTCCCTAGCCTGGCTTGCTGCATGCACTCTCAGGTTCACAGTTCCAGCCTGCTAGCTAGCTCAACTATTGGGGTCTCTTGTCTTTGGACCCTAGCAAGTTGTTCTTTGAGGCTTTTTGCTATCCTATATATCTTGCCATGACTTTCTCACCTTCCTGCCCCATTGCAGTTGCCCAACTATTTATTGACTCCAAGCCCTTCCTGAAACTATATTTTGTCATATCAAATAAAGCCAGAAAAAGAACAGGACTAAAGATTCAATTACTTCTGTCTGTTTAGGGCATGCATTGAATTGATGTGTCTAAATAGGCTCTGAGATGTATTGGGAGGCCCAGTCTTTAAACCATCCCTTAAAAAATATTTTTAAACACCTTTAGGAGCAGCAAGAATAGGGAACAATGGAACTGAGTTCTTTTCTTGATTCATGGTTCCAAGAAGGGCCTCTGGGGTGAAGGGGAGTACACTTGAGGACTCCTGTACTGTTGTTTCCACTTGCTGTGTGTGTCTAAGTTACCCAGACTTTTCTATATCCTATTCTCAACGTTGGCTAAAACAACTTGAGACTTGAAGCTTCTAGACTGTAGTCTGTACTTTATGCCAGAGAATAGTAGCTCTGTGGCTCCACTGACTTAGATTCAGGCTCTTCTGGGTCTAGGTCATCCTTGTAGGTCCTTTCTGACATAGAAGAAAGGTTGAGTCCTCTGTCTAGATGCCAGAAGGATTCGCAGCAATAGTAGGTGCTGCTTGGTAAAGAGGTGTTGGGGAAGGAGAAATGGCCACGGTTTGAGATGTTCTTCAGCCTTCTAAGATATGGGATGGGGCAAGGGGGACTAAGGAGACAGTGAATGCAACCTGCAGTGTGTGCCTGCCTTAGAGAAAACATACAGACTGCTCCCTGTCTTCTAGGGTCTAAGCCAATGAAGGACAGTTAACTGGAATAAGAGCTGTATAGATCAGTGTGGGAGCCATGCCTGTTTGCTGTCATCTATCATATCTCTGAGATTTTGTATACAGGGGGAGGGTGCCCTATAGGAGAGGGTATGCAGCTAATTCAGGTGGGGCTGGCCTAGGCTGATGCGCTGCTTAGCTCCACTCCAGGCTCCAGGACTTGTTGAAGGAGGAAGTACTTTACAGGAGAAACAAACGCACGGAATGGGCCCATAAAACCTTACTGCATTTCCTCTCCAGCCTTCCACAATGGGGTGATTTCCTGGAGCCAAGCCTAGGCCCCCCACACTGGAGGAGTGGGGAATCTGAAACTGGGCTAAGGGCTGCTCTACACTAGGACAGAAAGGAAACAGAGTGGCTCTGGGGAGGGGCAGGGAGATTCCTTTTTATGATTATTAATGCTTATGCTCTTTGAATTTATTAAAGGTCTGACTTCACTGC
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000022485:ENSMUST00000001709:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.684 A=NA C2=0.282
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0004624=Homeobox=WD(100=79.2)
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:
CTCCTCTGAACCCTGGGATGT
R:
CACTTCATCCTGCGGTTCTGG
Band lengths:
355-1047
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