MmuINT1020852 @ mm10
Intron Retention
Gene
ENSMUSG00000042448 | Hoxd1
Description
homeobox D1 [Source:MGI Symbol;Acc:MGI:96201]
Coordinates
chr2:74762980-74765142:+
Coord C1 exon
chr2:74762980-74763753
Coord A exon
chr2:74763754-74764054
Coord C2 exon
chr2:74764055-74765142
Length
301 bp
Sequences
Splice sites
5' ss Seq
AAAGTAAGG
5' ss Score
6.6
3' ss Seq
ACCTTGTCTTTATGTTGCAGGCA
3' ss Score
11.04
Exon sequences
Seq C1 exon
ATATGAAGCCACTATTTACCTCGGGCTCGCTCGCCATGGCTCGGCGAGGGCAGCGGGGGTAGCGGGAAGGCGGAGCTGCGCAGACCTGCAGGGTGCGGCGCCTAGGTCGTGCGGAGCGAGCCATGAGCTCTTACCTGGAGTACGTGTCGTGCGCCGCGGGCGGTGGCAGCGGAGGGGTAGGCGGCGACGTGCTCGGCTTCGCACCCAAGTTCTGCCGCGCCGACGCGCGCCCTGTGGCCCTGCAGCCGGCCTTCCCCCTGGGCAGCGGAGACGGCGCCTTCGTGAGCTGCCTGCCCCTGGCCACCGCTCGGCCCACGCCGTCGCCTCCCGCAGGCCCCGCTCAGTCCCCGGTCCCACAGCCCGCCGCGCCCCGGTACGCGCCCTGCACCCTGGAAGGCGCCTACGAGCGGGGCGCCGCACCTGCCTCTGCCGCCGAGTATGGCTTCTTGGGGTCCGGGCCGGCGTTTGACTTCCCGGGCGCACTTGGGAGAGCGGCGGACGAGGGCGGGGCGCACGTCCACTATGCCACCTCGGCGGTCTTCTCCGGCGGGGGATCATTCCTGCTCAGCGGCCAGGTGGACTTCGCTGCCTTTGGCGAGCCTGGCCCCTTCCCCGCGTGTCTCAAGGAGCCCGCAGACGGCCACCCCGGGCCCTTTCAGACTGTGTCCCCGGCCCCTGGAGCCTGCCCCAAGCCGGCCTCTCCCACCTCCAGCCTCCCGGCCGCCCACAGCACTTTCGAGTGGATGAAAGTGAAGAGGAACGCCCCCAAGAAAA
Seq A exon
GTAAGGAGGTGGGCGCTGAGGGGAGGCACCTGGGGGTTCGGGGGGGGGGGGCGCCTCCTTCGTGAAGAGCCGGGAGCGTGTGGCCACCAACCCTGGAGAGAGATTCTACTCCTAAGCCCTGGTCAGAGCCCAGGGTCAGAAAATGCCCCAGGAGCTGAGAGGCCTCAGCAGAGCGCTTCTTCTGGTTCAGCTGTGTCCATCACTCAGGAGGGCTGCGCTGTGACTTTGATTCTAAGTCTTAGCTCCACTGGATAGTTTCAGCATCTCCTCCTCCTGCTCACACCTTGTCTTTATGTTGCAG
Seq C2 exon
GCAAACTGTCCGAATATGGAGCCACAAGCCCTCCCAGTGCCATCCGCACAAATTTCAGCACCAAGCAACTGACAGAGCTAGAGAAAGAGTTTCATTTCAATAAGTACCTAACTAGAGCCCGACGCATCGAGATAGCCAACTGTTTACAGCTGAATGACACCCAGGTCAAAATCTGGTTCCAGAACCGTAGGATGAAGCAGAAGAAGAGGGAACGAGAGGGGCTTCTGGCCACAGCTGCCTCTGTGGCCTCGATTAAGCTTCCCCGGTCAGAAACAAGTCCCATCAAATCTGGCCGGAATCTAGGAAGCCCTTCTCAGGCTCAAGAGCCTTCCTGAGGCCCACTCTTAAGGCTGAGGACCTTGGGTCTACAGAAGTCACAGACTGCTCCCCACCTTTGAATAGACTTGAGAGCTTAGTTTGGGCTGGAGGTGGGCATGGGTAGAAATTAATACGGATTTTACTTGGCAAAGGAATTGTCTAAATTGGCTTCTGAGTTCCAGAGGCTGTGTATAGAGATATATATTTGATATCTTTTATTCGCATATTATTTTTGCCTCATGGGGAGGAAAGGTGTCTTAGCTACCTGCCTAAACGCTGCTATGTGAGCCACTTAAAATTCTCGGGTGCAGAGTGGCAGGCCTTCTTAGTCTAGTGTGGTCAGAAACGTATCTCTCTGAAGTTGTTTCAGTTTTAATTTCCTGGACAGACTACATATATTCAGCTTCCTGAGATGATCAAAGCTAGCTAGGGTTTCCTCTATGTAGCTAAGCTGCTTCAATGATGATCTTCATATTGTGCTCCAGTTTGTTTATTTAAAGTGGCGCTCCTACCTCTTCGTGTGCCTGGGTGAAGAAACACAATCACTGTTTAGTTAGTAGCGGAACAAATCCACAGGGTAGGTAAGGATTAGAATCTGAATTATACCTTGGCATCAGTTACTCAAACTTGAAGTGTAAATATATACAGTATGTATATTTTTTAAAGATTTGCTTGCAGTGAACCTTATATATGACATTTAATGTCATGCATAGCATGTAAAGATTTTGACTTTTTTTTTTTTTTTTTGGTAATAAAAGTTACAGAATCTA
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000042448:ENSMUST00000047793:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.257 A=NA C2=0.550
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0004624=Homeobox=WD(100=50.0)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Rat
(rn6)
No conservation detected
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GAAAGTGAAGAGGAACGCCCC
R:
GCCTGAGAAGGGCTTCCTAGA
Band lengths:
348-649
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- 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