MmuINT0078769 @ mm9
Intron Retention
Gene
ENSMUSG00000001656 | Hoxc11
Description
homeobox C11 [Source:MGI Symbol;Acc:MGI:96193]
Coordinates
chr15:102784957-102787132:+
Coord C1 exon
chr15:102784957-102785638
Coord A exon
chr15:102785639-102786899
Coord C2 exon
chr15:102786900-102787132
Length
1261 bp
Sequences
Splice sites
5' ss Seq
CCAGTAGGT
5' ss Score
5.41
3' ss Seq
TGCCCTTCCCCTCCCTCCAGACG
3' ss Score
12.3
Exon sequences
Seq C1 exon
ATGTTTAACTCGGTCAACCTGGGCAACTTCTGCTCGCCTTCGCGCAAGGAGAGGGGCGCTGACTTCGGCGAACGAGGGAGCTGCACCTCCAACCTCTATCTGCCCAGTTGCACTTACTACGTGCCTGAGTTCTCCACCGTCTCTTCCTTCCTACCCCAGGCTCCCTCTCGTCAGATTTCTTATCCCTACTCAGCCCAAGTGCCCCCGGTCCGGGAGGTCTCCTACGGCCTGGAACCGTCCGGGAAGTGGCACCATCGGAACAGCTACTCGTCTTGTTATGCGGCGGCCGACGAGCTTATGCACCGGGAGTGCCTGCCTCCTTCCACAGTCACTGAGATCCTCATGAAAAATGAAGGCTCCTACGGCGGCCACCACCACCCCAGCGCCCCGCACGCGGCCCCCGCCGGCTTCTACTCCTCAGTCAACAAGAACAGCGTCTTGCCCCAAGCTTTCGACCGCTTCTTCGACAACGCCTACTGCGGTGGGGGAGATGCGCCCGCCGAGCCCCCCTGCTCCGGCAAGGGCGAGGCCAAGGGGGAGCCTGAGGCGCCCCCCGCCTCGGGACTTGCGTCCCGGGCAGAGGCCGGTGCTGAGGCCGAGGCCGAGGAGGAGAACACGAATCCCAGCTCGTCCGGTTCTTCCCACTCGGCGACCAAGGAGCCGGCCAAGGGAGCCGCCCCCA
Seq A exon
GTAGGTAGCAGCGGCCGGGAACCCGAGGGCAGCGAGGGAGGGAGCGGAGAGGGAGGGCTGGAGTAGTGGGGGGGGGCAGGGGAGCGCGGACAGCCTCGTGTTTTGGGTCAGTCTGATTTTATGTGGAGTTTTATAAGCATTCAAAGGATTTTATTATAACCTACAAAGCCCTCTCTCCCAACGACTCGACTTTTTACGATGGAGAAGGGGTGGGGAGGGAGGGAAAGGGGCTCTTTGGAAAAGCCGGGTGAGCCCCCCTCCTCCGTTATCTCCCTCGGTCTGTGAAATTTTTAAAAGTGCCACCATTGCGGGCGATATTAACTTTGATCGTGAACTTAGAGGAGCGTTTAAGAAAGGATGGGGAGTCGGACTGCTGGGGGGTTGGGAGGGAGGGGAGGGGTGGAGGGGGAAAGGGGAGGGCGAGGGACAGACTGGGAGAAATCCAGAGAAGGGGAGAGGTAAGGAACAGAAGCGACGCGGCAGAACTGGAGTCCAGGGAAGCTCTCCAAGGCCGCTCCTCTTCTTTTTAAAACGACTTTTAAAAATGTTCAAATTACGTGTTCGCGGGTCTTTGAGAAGAAACCGGGGCAAGCCGGGGTTTGGCGGTGGCAGGAGAGTGGGGAAAGAATCAGAGATTCCCTTGCTCTGCAGGGGAAGGTAGCGGTGGCTCTCCAGGGTCCGAGGCCTCTCTCTGGGTAGGCCCAGCCTGACTGTACGCAAGCCTGGGGCAGGCAAGCGGCTGGGTGTCCCAGGGCGCCAGGGCACCACAGGAGGCTCGTAGGTGTCCTGCTACCTCTACGGGCTAGTTTGCTCCCGATTCCTCACTGCTCTCTCCTGATCTCACTCCTTCGCGCCGATTCTCCGCGGTTCCCTCCGATTTCTGGAGGAAGGGATCCTGGATTTGCAGAAGCATTAGGAGGGCGGCTTGGAAAGGGCAAGGGCAGCGACCAGGAGCAGACAGAGCACCCCAGGGAAAGCACGTGGCTCAGGCAGGCTTTCCTCCACCCTCAGACCTTGTCAGCTAGGGCTCTGGCCTGAGGGGCAGGGGGAACTAGGTTCTCAGTGAACCTGGCGGTGGGATCAAGGCTTGCCCCAGCGCAGCGGATACGGAAGAGGAGCCGCCGGCCTAGAGGGAGGGCTGCCCGGCAGCGGGACTGGGAGCTGTGTAGCTGAGCTTTCAGCGACTGGGTTGGCTGGGGTCTCCCGGGGTCTCACGTGTCTCTTTCCCCTCTCCTCGCACTTGCCCTTCCCCTCCCTCCAG
Seq C2 exon
ACGCCCCCCGCACCCGCAAGAAGCGCTGCCCTTATTCGAAATTCCAGATCCGGGAACTGGAGCGAGAGTTTTTCTTCAACGTGTACATCAACAAAGAGAAGCGGCTGCAGCTGTCCCGGATGCTGAACCTGACAGACCGACAAGTGAAAATTTGGTTTCAGAACAGGAGAATGAAAGAAAAAAAACTGAGCAGAGACCGGCTGCAGTATTTTTCAGGAAATCCACTGCTGTAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000001656-Hoxc11:NM_001024842:1
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.399 A=NA C2=0.195
Domain overlap (PFAM):
C1:
PF120453=DUF3528=WD(100=62.7)
A:
NA
C2:
PF0004624=Homeobox=WD(100=73.1)
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:
CCGGCTTCTACTCCTCAGTCA
R:
AAAACTCTCGCTCCAGTTCCC
Band lengths:
351-1612
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: