MmuALTD0002951-3/3 @ mm10
Alternative 5'ss
Gene
ENSMUSG00000029646 | Cdx2
Description
caudal type homeobox 2 [Source:MGI Symbol;Acc:MGI:88361]
Coordinates
chr5:147300805-147303326:-
Coord C1 exon
chr5:147303219-147303326
Coord A exon
chr5:147303181-147303218
Coord C2 exon
chr5:147300805-147302093
Length
38 bp
Sequences
Splice sites
5' ss Seq
CAGGTGGGA
5' ss Score
6.71
3' ss Seq
TTCTATTTTGTCATCTCTAGGTT
3' ss Score
11.88
Exon sequences
Seq C1 exon
TGAAAACCAGGACAAAAGACAAATACCGGGTGGTGTACACAGACCATCAGCGGCTGGAGCTGGAGAAGGAGTTTCACTTTAGTCGATACATCACCATCAGGAGGAAAA
Seq A exon
GTGAGCTGGCTGCCACACTTGGGCTCTCCGAGAGGCAG
Seq C2 exon
GTTAAAATTTGGTTTCAGAACCGCAGAGCCAAGGAGAGGAAAATCAAGAAGAAGCAGCAGCAGCAACAGCAGCAGCAGCAACAACAGCCTCCACAGCCGCCGCCACAACCTTCCCAGCCTCAGCCGGGTGCCCTGCGGAGCGTGCCCGAGCCCTTGAGTCCTGTGACCTCCTTGCAAGGCTCAGTGCCTGGTTCTGTCCCTGGGGTTCTGGGGCCAGCTGGAGGGGTTTTAAACTCCACTGTCACCCAGTGACCCCTCCCGTGGTCTGAAGCGGCGGCGGCACAGCAATCCCAGGCTGAGCCATGAGGAGTATGGACGCTGCGAGAATCCTCAGAAGAGATTCCTCTCCTCCTACCCACGAACAGCATCTACTGATGGAGATTGAGGACAGAAGATGAGTGGAATTATGGACCTCAGGGGAAGACATGGTTTAGATTTTTTTTTTCTTTTTAACTTTTCCCATTCCGACTCTTCCTGCCAGCAACGACAAACGAAGTGAT
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000029646-6-2,7-2,8-2-3/3
Average complexity
Alt5
Mappability confidence:
NA
Protein Impact
Protein isoform when splice site is used (Ref)
No structure available
Features
Disorder rate (Iupred):
C1=0.306 A=NA C2=0.904
Domain overlap (PFAM):
C1:
PF0004624=Homeobox=PU(73.7=85.7)
A:
NA
C2:
PF0004624=Homeobox=PD(22.8=15.5)
Main Skipping 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:
GTGTACACAGACCATCAGCGG
R:
TTTTCCTCTCCTTGGCTCTGC
Band lengths:
119-157
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