MmuINT0078755 @ mm10
Intron Retention
Gene
ENSMUSG00000038236 | Hoxa7
Description
homeobox A7 [Source:MGI Symbol;Acc:MGI:96179]
Coordinates
chr6:52216009-52217297:-
Coord C1 exon
chr6:52217030-52217297
Coord A exon
chr6:52216031-52217029
Coord C2 exon
chr6:52216009-52216030
Length
999 bp
Sequences
Splice sites
5' ss Seq
CAGGTAGGC
5' ss Score
9.88
3' ss Seq
GTCCAAATTTCTGTTCCTAGGAC
3' ss Score
8.56
Exon sequences
Seq C1 exon
AGAAGCGGCTACGGGCCGGGCGCCGGCGCCTTCGCCTCCACTGTGCCGGGCTTATACAATGTCAACAGCCCCCTCTATCAGAGCCCCTTCGCGTCCGGCTATGGCCTGGGAGCCGACGCCTACAACCTGCCCTGCGCCTCCTACGACCAAAACATCCCCGGGCTCTGCAGTGACCTCGCCAAAGGCGCCTGCGACAAGGCGGACGAGGGCGTGCTTCACGGCCCGGCCGAAGCCAGTTTCCGCATCTACCCCTGGATGCGCAGTTCAG
Seq A exon
GTAGGCTCAGTGGTCGGCGGGGTCGGCGAGCGGGAGGAGCGGAGGGGCGGGAGCAGGGCGCGGGGGGCTGAGAGAGCCCAGCCCGGCGGCTTCCAGCCGGCGGCCCCGCAAGTCCCCGTGGCGCTGCCTTTCTGGTTTTAATTAGAGCTGAGGCGCCATAGCGTGGAGAGACCCGTAGCATTGTATGTAAATGAGGCTCATAAAACTTTTTATGGCCCAATTAATGGGTTCGATCCTCGTAAATTTATTTAACTCCATTTGCCTTGGAATTTTTACAATAAGTTTCTCCGCTATTCTCATTCTCATATTCTCTCTCTTTCTCCCCCCCCTCTCCCCCTTCTTCCCTTCCCTCTCTTTTTCTCTCCCTCAGTCTTTCTTTCTATCCCCCTCTTTTCTGTCCTCTATCTCTTTCTTGACTCCAGCTCTCTCTCCCCTCCTTCCCTTCTTTCGGCCTGGCTTTCTTTCTCAAAGGCAAGGAGAATTGAGACCTCCGGGATCCCTCACTCATCACTGTACCAGAGGCCATTTCCAGAACGGGGCTGAAGCCAATGGGACAGAGGGTGGGAAAGTCACAGGAAGGTCTTGTGGATGGGGCTGCTGATGAGGGTCGCCCACTAGCAAGGCTGGGGAGCAGCCAGGCTCGCCTTTGAATGGCAAAAGCGCAGAGTCCCCCACTTGCCACACTCTATATTGACAATTTCCCTTTGTCAGGGGGAAGCAGGACATTGTGGAAACGTAGCCGGCTGGAAAGGCCAGTTGTAAAGTTGGAATTCTGCCCTAAGGCTTCTCACAGATGTTCTTGCTTGTCTGGCCCTGGGGCCTTCCGCTCACAATTTCCCTCCCCCAGCTCAATTGAGGGTGATGAGGGTTGCACCTGGATTTGGGCAAGGTGGAAGGTGCAGGTTCTTGGGCTGCTGGCCTGACTAAAGCACTCTTCTGTCCACATCCTAGTCTGCTTGTCTGTTTTGTCTATCTATATGTCCAAATTTCTGTTCCTAG
Seq C2 exon
GACCCGACAGGAAGCGGGGACG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000038236:ENSMUST00000150041:2
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.583 A=NA C2=0.701
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GCCTTCGCCTCCACTGTG
R:
GTCCCCGCTTCCTGTCGG
Band lengths:
262-1261
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