MmuINT0078775 @ mm9
Intron Retention
Gene
ENSMUSG00000001657 | Hoxc8
Description
homeobox C8 [Source:MGI Symbol;Acc:MGI:96198]
Coordinates
chr15:102820970-102824685:+
Coord C1 exon
chr15:102820970-102821646
Coord A exon
chr15:102821647-102822993
Coord C2 exon
chr15:102822994-102824685
Length
1347 bp
Sequences
Splice sites
5' ss Seq
ACGGTGAGA
5' ss Score
8.94
3' ss Seq
TGGGGTTCTGTTCTGTTCAGCTC
3' ss Score
6.84
Exon sequences
Seq C1 exon
TGTTAGAGGAAAGAGCTAAGTGAGAGCGCGCGCTCTACCTACCGACAGTGAGCAGAGAGCTGCAGCCGCCCGAGCCCGCAGCCGGCACCGCGCCCCCACCTGCCCAGCCCCCAGCCCAGCAGTCCAGCCCGGGGGAGCCGGCCAGCTTGGGGTTCGGTCCCGGGGGGAGGGGAGTTTCGGGGATACCCGGCGGGGGAGCGTGATCCAAGGGGAGGGGGCCGCGGGTTTTCATGTACCCAGCATGAGCTCCTACTTCGTCAACCCCCTGTTTTCCAAATACAAAGGCGGCGAGTCCCTGGAACCGGCCTATTACGACTGCCGGTTCCCTCAGAGCGTGGGCAGAAGCCATGCGCTGGTGTACGGGCCCGGCGGCTCCGCGCCCGGTTTCCAGCACGCCTCGCACCACGTCCAAGACTTCTTCCACCACGGCACCTCCGGCATCTCCAACTCGGGCTACCAGCAGAACCCATGCTCGCTGAGCTGCCACGGAGACGCCTCCAAATTCTATGGCTACGAGGCGCTCCCCAGACAGTCCCTTTATGGGGCTCAGCAAGAGGCGAGCGTGGTGCAATATCCCGACTGTAAATCCTCCGCCAACACTAACAGTAGCGAAGGACAAGGCCACTTAAATCAGAACTCGTCTCCCAGCCTCATGTTTCCATGGATGAGACCCCACG
Seq A exon
GTGAGAAGCCTTTTCTCTTTCCCCCTTGGTCTCCCGCGCTCCGGGGTCTTCCCCCCTCCCTCGCCTCCTTTTTGTCTGCCCTAGCTCGCTTTCCTTCCTGGCTTTGGGGGTCTCTCCCACTCCACTCCCGTGCCTGGGTGGGTTCCTGGGAGATTGAAAGGCTTGGCTGGGGGTGGAGCGTGGGGTGCCTGAGACATTGTGCTTGTTGGGGTGAAGGTGGGGGAAAGGTGACTTGTGGGTGCAAAGGGTTAAAAATCGTTTTCTCTATTCCTTCTGTCTCTCCTTCTTCCCATCTGTAAAGCCAAAGTTGGGGAGATGGCTGGCAAGGACACCCTAAGTAAACTGAGGTTATCAGTCTTTGGGGTTGGTAGCCAGTTTTCCCAAAGACATTTCCCAACGCCAGCCATCCCAAGACAGTGACCAGACTGTTGGGTGAAAAGGAGACCCTTTGCTATCTCCCCCTAGTCAGGGAGAGGGGCAAGACCTCCCCTCTCCCAAGGACAAGCATTCTGCCTCTCTAGGATTGTCACTTCTTCCCCTCAGAGAAGCAGCCTGAAGGCCACTACCCCAACTTTTCTGTACTTCCTCCAATTGAAGAGAAGACTGAAAGCCCGAGAAGAGGAAAATGATTGCTCAAAAGGAGAGAGGGGTCATACCAAGTAGGGGCCTCTGAGATCCAGGGTACTCGAGTCAGGCTACCCGCCAATCAAGAACTATGGAGTCTCTTGGAAAGCTGTTTAGGTCATGAGCCCCTCCAAGGGTGGCCCTTCATGGCCCAATTTCGAAGTACAGGGGGAAGAGATAACGACAAGTTCCGGCAGGGATGGCCCTTGATTTATTTTTGGTCTCCAGTTAGCAATCAGGCAGAGCAGTGATACATTCCAGAAGATCAATTATTTTTCTTATTGGAAAAGCATTAGTCAGAGATCGGCAAGGAGGGGGCAATTGGCACAGCCCCCTCTCCTTTAACCCCAGCCCTTTTCCTTTCTTTTGGAAACAGATTATTTCCCTAGGCCGCCTCACTAAATGCCATTCTGCACTTGTAAACAAAGCTGCAAGGGCTAAGCTGTAGGCCTGAGGGACCCTGATGGCTTCCTTGTCCACCTCAAGCCCTTACTTTTCAGACAACCACGTCCCAGCCCCCACCGTCACCCACCTCCCAAGGTGAAGGAAGTCAAACCAAAACAGCTATGGAAACTTTTCCTGCCCTTGCTTGCCTTCTGCAGTCGGCCTTATCGGCAGGAGGGAGGGAGAACTGGGAATAGCAGAGAGGGAAGTTTGTGGGGCTGTGTTGGGGGGCGGAGCCCCCACCCAGACATAACCAGACTGGGGTTCTGTTCTGTTCAG
Seq C2 exon
CTCCTGGGCGGCGCAGCGGTCGACAAACTTACAGCCGGTATCAGACCTTGGAACTAGAGAAGGAGTTTCTCTTTAATCCTTATTTGACCAGAAAGCGCCGGATTGAAGTCTCTCACGCCCTGGGACTGACAGAAAGACAAGTGAAGATTTGGTTCCAGAATCGAAGGATGAAGTGGAAAAAGGAGAACAACAAGGATAAACTGCCTGGGGCCCGAGATGAGGAGAAGGTGGAAGAAGAAGGGAATGAGGAAGAGGAGAAAGAGGAGGAGGAAAAGGAAGAAAATAAGGACTAAGGAAAAAAAGAGAGAGAAAATCAGCCCCCCCCCCAGCAACTCCCTTGAAGTTTCGTTTTATGGTAGCAGATAAATTGAGAAGTTTACGACTGTCATTTGCTTTTATAGAGAATAGAATGACACTCACAACTCTAACTACCTGTCAGATAGTTGCAGCTCTGCTTTTATTACCTTTGGGCTTCCCCCACTCTTTATTTGTCTGGGGGTTGGGAGGGGGAACCTGAGACACAGGGAAAAGTTCTGTTCTACTCCATGCCCAGCATACACTCTCTTGTTCCTGCTCCCACCTTCTGAGCCCTTCCCCATAAAGTCTAACCCTTCACACACACACACACACACACACACACACACACACACACACACACACACACACTTCTCTCCACACTCCCTCTTCACGGTGCTTCTCTGGTATTTATTTTAAAAGGGATTCCCCTGAAGATATAGAAGATGATTCCTGGCTTTGCTTGTATGCTGGGAATTAGAATACTGGATAAACAGTTTTTTTTTAATGAAAAGAAAGAAGGAAAAAAACAGGAAAGGGGGAAATGAAAGGAAAAATTAAAAAGAAATAAAAGATAGCAAAGAAGATTCCCCTCCCCCTCTGAGGCTCTTTCCTTAGAAAAACCCCCTTGACTTTCTCCAGGAATCTGCTGGAAATCAAGGAGATGTGGGTTTCTCTACCCACCTCCTTCCTGAGGGGTCTATTAGAACTGGCAATGGTCTCTGAAATCCTACCTATCCATCCCATAGTCACTTGGGTCCATGCCTTCCTTGCCTTGCCTTTGCTGTTTGATCTTTTGGGCCCCCGGCTTCCTCTGAGCTGTGTTAGTGTTTGTGCTCAGAAGTCACCATAATCATGAAAATAATATACTGATAATAAATCTTTAACATACTACCTAAAGGGAACCTGCAATAATCTTGGGGGAAAAAAAAAAAAGAAAGAAAAATTCCTAATACAGGAGGGAGAAAAAAAAAAAGAAAAAAAAAGAAAAAAAAGAAAAAAGGAAGAAACCTCCAGCGTATTTTATCACTACCTATAGAAAGAAATCCTGCTTTGAGAGTATTTGTAATGCGGTTTTGTTGTTGTTTGTTGCTGCTTCTTTCACTAAGAAAAAAAAAAATCCCAACAACTGAGACTGCCTAGCCCGCCGGTCTTGTGCGCTTTTATTGTGCTTCTAACCCCAGTAGAGTAGAACTAAACTGCACTGAATGTATAGTTACTCTGTCTTGAATTCTCTGTTTATGCAATGTGCTCGAAAGGAAAAAAAAACGTTAAAATATATCTATAATAATAATTTTGGTCATTTGTCTTTATGTCCAGCTATGAATGTAGATTTTGTGTCCTGAAAGCTCTGTTCCTGGTCCAAGTACTTTGTATTGTATACGTGAGTCATAATAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000001657-Hoxc8:NM_010466:1
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.253 A=NA C2=0.526
Domain overlap (PFAM):
C1:
PF095335=DUF2380=PU(74.1=56.8)
A:
NA
C2:
PF095335=DUF2380=PD(25.0=28.6),PF0004624=Homeobox=WD(100=58.2)
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:
CTACCAGCAGAACCCATGCTC
R:
GCGTGAGAGACTTCAATCCGG
Band lengths:
342-1689
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: