MmuINT0078789 @ mm10
Intron Retention
Gene
ENSMUSG00000101174 | Hoxd4
Description
homeobox D4 [Source:MGI Symbol;Acc:MGI:96208]
Coordinates
chr2:74727074-74729123:+
Coord C1 exon
chr2:74727074-74727705
Coord A exon
chr2:74727706-74728261
Coord C2 exon
chr2:74728262-74729123
Length
556 bp
Sequences
Splice sites
5' ss Seq
CGGGTAAGG
5' ss Score
10.17
3' ss Seq
TTGTATGTTTTGTCTCATAGTGA
3' ss Score
8.18
Exon sequences
Seq C1 exon
ACTTGATTACACGTATGTTATTTAGTTAAATTTGTGAAAATTATGAGATGCTCACCAACCCGGTGATAAACATGCTTTCTTCCTATTGGCTGGCCTGGTCACATGGCCGCCCAACTTTATTCAGTTGACAGCAAGTAGGAGGGCCCAATGGAAGGAGAAAAAAGACAACACGAGAAAAATTAGTATTTTCTACCTTCTGAAATTAATGGCCATGAGTTCGTATATGGTGAACTCTAAGTACGTGGACCCCAAGTTTCCTCCGTGCGAGGAATATTTGCAGGGTGGCTACCTAGGCGAGCAGGGAGCCGACTACTACGGCAGCGGTGCACAGGGCGCCGACTTCCAGCCCTCGGGGCTCTACCCACGGCCCGACTTCGGCGAGCAACCCTTCGGAGGCGGCGGGCCCGGGCCTGGCTCAGCGCTGCCCGCGAGGGGTCACGGACAGGAGCCGAGCGGCCCGGGAAGTCATTACGGTGCCCCGGGAGAGCGGTGCCCAGCGCCCCCGCCTGCGCCCCTGCCTGGCGCTCGGGCCTGCAGCCAGCCCACCGGCCCCAAGCAGCCGCCCCCCGGGACAGCACTCAAGCAGCCCGCTGTGGTCTACCCTTGGATGAAGAAGGTGCACGTGAATTCGG
Seq A exon
GTAAGGAGTGGGGGCAGCGACCTCACAGCCCTCCCGCACCACTCCTTGCATCTTTTGGCCTGCACCCCCCACCCCAGGGGTTGCGAATGGGTAGGGGCTTGTGCAGCTTCCTTGGGCGCCGCAATTACTCTCTCCATAAATTTTTATAGCTGAGGGAGCAGGCCGGGACCATGTGGCTGGCTGCTTGGCTGTGGGCGCAAAAGGGGGTGGGGATGGGGATGGGGTGGGGGGAGGACTCCATTTCCACAGCAGAGGGAACGCAGAGCAAAACAAGGACCTTTCCAAAATGTTGGCGATACCGAGCTCTTGGTGGGCCAGTGGCAAGGGAGAACCTTTGAGGAGGACCTGTGAGCGTGGGGAGTGTGTGCATGGAAGGGCTTGGGTGGGAGTGTGTGTATGTTTAGGGAGAGGGCGGGAGGGAGGAAGCTGGCCAGCTTGGAGCACAGGGGGGGCCCGAGGGCTGCGAGACGCGCCAGGAAGTGAGGGCAGAGGCAAGCCTGGGGCCTAACTAGTGGCCGGGCTCTGACCTGGCTGTCTTGTATGTTTTGTCTCATAG
Seq C2 exon
TGAACCCCAACTACACCGGCGGGGAGCCCAAGCGCTCCCGGACGGCCTACACCAGACAGCAAGTCCTAGAACTGGAAAAGGAATTTCATTTTAACAGGTATCTGACCAGGCGCCGTCGGATTGAAATCGCTCACACCCTGTGTCTGTCTGAGCGCCAGATCAAGATCTGGTTCCAGAACCGGAGGATGAAGTGGAAAAAAGACCACAAACTGCCCAACACCAAGGGCAGGTCTTCTTCCTCATCTTCCTGCTCCTCTTCAGCTGCCCCGGGCCAGCATTTGCAGCCAATGGCCAAGGACCACCATACGGACCTGACGACCTTATAGAAGTGGGGACCCTGGGCCTATCCCTTCTTGCACTCCAGGTTGAGGCGAAGCTGCGGGTGCAGGCGGGGCCTGCTGTCACCTCACTGGGCTCTAAGGTACTGTGGGGGTGGACCTGGGACCTGCAGGCCGCCCTCGGACTAGGTTACCTTCCTGCCCGAGGGCAGCCCCCTCCCTAAAGTGGGGAAGGGTGGGAGGGTGGGCGGGCTTCTTTAAGTAGATTATCATATGGCAGGAGCTACTGAGAACATAAACCCTTGGCGAGTCATTAAACTCCTGAAAATCTCTGCTGGTGGATTGAATTTGCAAATGAAGGTTGGAGGCTTTACCCCAGTGGGAACCGGGATGGTCTCCTCCACACCACCCCCTTCAGGGAGCTGTGTGGCTTAGTAACTGTGGGGGAGTTGAGGCAGAAGGCCAGCCAGTGCTAGGTGCTTTCAGTGCAAGCAGGAGAGGCTGAGCCAGAATCCCAGAACTTTCTGGATTATCTATAGAATTTCTTCTGTGATTTAAAAAAAAAAAAAAAAGAAAGAAAGAAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000101174:ENSMUST00000111980:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.727 A=NA C2=0.620
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0004624=Homeobox=WD(100=52.3)
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:
TGGATGAAGAAGGTGCACGTG
R:
CAGGTCCGTATGGTGGTCCTT
Band lengths:
342-898
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