MmuINT0033998 @ mm9
Intron Retention
Gene
ENSMUSG00000031326 | Cdx4
Description
caudal type homeobox 4 [Source:MGI Symbol;Acc:MGI:88362]
Coordinates
chrX:100523348-100525563:+
Coord C1 exon
chrX:100523348-100523493
Coord A exon
chrX:100523494-100524772
Coord C2 exon
chrX:100524773-100525563
Length
1279 bp
Sequences
Splice sites
5' ss Seq
CAGGTATTA
5' ss Score
7.26
3' ss Seq
TAAAGCATTTTGTATTTCAGGTG
3' ss Score
8.25
Exon sequences
Seq C1 exon
GGAAAACCAGGACAAAAGAAAAGTATCGTGTGGTCTACACAGATCATCAACGGCTGGAGCTGGAAAAGGAATTTCACTGCAATAGATACATCACCATCAGGAGGAAGTCAGAGCTGGCAGTTAACCTGGGCCTTTCTGAGAGACAG
Seq A exon
GTATTACCAACATTCCCACATAGTTATTTCAATCGGCTAGGGTTTGGAGGAAATAGCAAAACAGAAGACAGATGCGTTTCTAAGTGCTCCTAAACCCATACTCACCCTGGGTTGTTTCATTGATCAGGGGACTTATTAGCTATTTAATGGGTGGGTATTTTGTGAGCCTGGGAGCAAGAGATCAAGCAGAGAGGTGCAAAGAGATTAGAAGTCCAATATAATTCATCAATCAAGTCAAACGTTGATCTGGTCCCTCAAGTAGTACTAACGAGTGTGAAAAGTGGAAATTTCACAACTGTGGCCACTGTCTGAGTCCTATCAGTCAAACTACAAGAGGAACTACATATCAGTGCAGTTCTGTGGATGGAGCTTTTCTGTTATTCAAAATAGGAAATGTAACCTTCTCTGGTCTGTATGATGTTATGATGCCTGCCTCCAATTTAGCTTCCTGTAAATACTCAATAAAGATCAACTTACAGCAAAGGGCAGCAGTCTCCACTCATTCAGACTTGGCAATTACACGAGCACCTGGTGAGTTTTCCCTAAGTCTAAGAATGATGCTGGAATCATAGAAGTCTAGAAATGTAAAATTCATTAATGCATTGCCTTATCTCAAGCAGTTTGCATTCCAACCACGTATAGGCGCATTAATACCACTCTCGTGTTGATTTACAACAAGAAATAGATGGTATTTCATGACCATGTTCACCCAGTTCTCGGTGTTAATTTTTTTTTTAATGGTTTTTCGAGACAGGGTTTCTCTGTACAGCTCTGGCTGTCCTGGAACTCACTCTGTAGACCAGGCTGGCCTTGAACTCAGAAATCCACCTGCCTCTGCCTCCCAATTGCTGGGATTAAAGGCATGCGCCACCACGCCTGGCTCGGTGTTAACTTTTTAATATAAGAAAAATTTTCTTAATGGCCAACTGTAATCACTGTTGCCATTTAAATCATTCTCTTTCATCAACATTCCTCAGCATCATTATATAATTATTTCTACTTGTGTAACAGAGGATGCAAATGAGTTGTAATACATATAGCTCTGTATTCAGAGTCGGTAGTCCTAGGTTTGATGGCTTCAGTCTCATCTCTTACAAAGCACCTTCTCTTTCTGAGACACAGTGTTTTCAAACCTGTAAAATGGGTATAGTTATAGGCAAAGTCACCCTAAGGCTCAAATGAAGTGATGTGTGTGAAGGAGGCTTGTAAGGCTGCACTTGCTGTGTTGGTTACACTTAGGGTGTTGTTCCCATTAAGTATAAAGCATTTTGTATTTCAG
Seq C2 exon
GTGAAAATCTGGTTTCAGAATCGCAGAGCCAAGGAGAGGAAGATGATAAAAAAGAAAATCTCCCAGTTTGAGAACACTGGAGGTTCCGTGCAAAGTGACTCTGGCTCCATCAGCCCCGGAGAACTGCCTAACGCTTTCTTCACCACTCCATCTGCTGTCCGTGGATTTCAGCCAATCGAGATACAGCAGGTCATAGTTTCTGAATGAAACAGGAGCAGAGAAACGGAAGCATCCTTCCTGTTACAGTGTCTCTTTGGCCTCTAAGCTAACAGCAGGGCAGTTGAGATTGGATATAATTCCTTACAAGACACAATTCCAAACAAGTAGACACACGATGAGTTGGAGATATTTCAGAAGACTCTAATATTCAGAAACCATCCCCAGACCACTCTTATTCCATGCTGTCATATGGGGGCTGGGCAAAAAGCTGTGTGAAAAGCTTTGCTCCTTAAAGTCTAGACTCAAGAGCCCTTGAAACTTTGTTCACAATTTCAGAAACTTGTTTGTGCATATGCTCTTGTATTTGTTATTTGATTTTGGTCTTTTTAGGGAATAGGAGTAAAGTAAGCATAAATTTCTCTATCTGGAGGTATCTTTTGGCGAAGAAATTAAAAAACAACCAGTTTTACAAGATAACTTTGTAAAACAGCATCAGGAGGTGATTACAAATCTATTGCCATTGGTTAATTAAATGAAGATCATTTTTCCCATTGAATAATACTCACATGCTATCAATTACCTAGCCATAGAACTTAGAAGATTTATCTATTTCAAATCTTGTCAAAACAATG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000031326-Cdx4:NM_007674:2
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.122 A=NA C2=0.309
Domain overlap (PFAM):
C1:
PF047317=Caudal_act=PD(1.9=6.1),PF0004624=Homeobox=PU(73.7=85.7)
A:
NA
C2:
PF0004624=Homeobox=PD(22.8=18.8)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Rat
(rn6)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TCAGGAGGAAGTCAGAGCTGG
R:
ATCCAATCTCAACTGCCCTGC
Band lengths:
342-1621
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: