Special

MmuALTD0002951-2/3 @ mm9

Alternative 5'ss

Gene
ENSMUSG00000029646 | Cdx2
Description
caudal type homeobox 2 [Source:MGI Symbol;Acc:MGI:88361]
Coordinates
chr5:148112381-148114902:-
Coord C1 exon
chr5:148114795-148114902
Coord A exon
chr5:148114761-148114794
Coord C2 exon
chr5:148112381-148113669
Length
34 bp
Sequences
Splice sites
5' ss Seq
GAGGCAGGT
5' ss Score
1.9
3' ss Seq
TTCTATTTTGTCATCTCTAGGTT
3' ss Score
11.88
Exon sequences
Seq C1 exon
TGAAAACCAGGACAAAAGACAAATACCGGGTGGTGTACACAGACCATCAGCGGCTGGAGCTGGAGAAGGAGTTTCACTTTAGTCGATACATCACCATCAGGAGGAAAA
Seq A exon
GTGAGCTGGCTGCCACACTTGGGCTCTCCGAGAG
Seq C2 exon
GTTAAAATTTGGTTTCAGAACCGCAGAGCCAAGGAGAGGAAAATCAAGAAGAAGCAGCAGCAGCAACAGCAGCAGCAGCAACAACAGCCTCCACAGCCGCCGCCACAACCTTCCCAGCCTCAGCCGGGTGCCCTGCGGAGCGTGCCCGAGCCCTTGAGTCCTGTGACCTCCTTGCAAGGCTCAGTGCCTGGTTCTGTCCCTGGGGTTCTGGGGCCAGCTGGAGGGGTTTTAAACTCCACTGTCACCCAGTGACCCCTCCCGTGGTCTGAAGCGGCGGCGGCACAGCAATCCCAGGCTGAGCCATGAGGAGTATGGACGCTGCGAGAATCCTCAGAAGAGATTCCTCTCCTCCTACCCACGAACAGCATCTACTGATGGAGATTGAGGACAGAAGATGAGTGGAATTATGGACCTCAGGGGAAGACATGGTTTAGATTTTTTTTTTCTTTTTAACTTTTCCCATTCCGACTCTTCCTGCCAGCAACGACAAACGAAGTGAT
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000029646-7-2,8-2,9-2-2/3
Average complexity
Alt5
Mappability confidence:
NA
Protein Impact





	

	
Protein isoform when splice site is used (No Ref, Alt. Stop)





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 Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000031650





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
NA
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chr13:27964874-27965015 
ALTERNATIVE
HsaALTD1032780-1/2
(CDX2)
Human
(hg19)
chr13:28539009-28539010 
Rat
(rn6)
chr12:9467817-9467958 
LOW PSI
RnoALTD0006186-1/2
(Cdx2)
Cow
(bosTau6)
chr12:32321317-32321458 
LOW PSI
BtaALTD0004936-1/2
(CDX2)
Chicken
(galGal4)
chr1:175317561-175317562 
LOW PSI
GgaALTD0006647-1/3
(CDX2)
Chicken
(galGal3)
chr1:180355204-180355205 
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected




Primers PCR

	

		

			
Suggestions for RT-PCR validation

			

				
F: 
GTGTACACAGACCATCAGCGG

				
R: 
TTTTCCTCTCCTTGGCTCTGC

				
Band lengths: 
119-153

			

		

	





	
Functional annotations
(Submit an annotation)

	


There are 0 annotated functions for this event 


		










GENOMIC CONTEXT[edit]












INCLUSION PATTERN[edit]






SPECIAL DATASETS
  • Pre-implantation embryo development
  • Neural differentiation time course
  • Muscular differentiation time course
  • Spermatogenesis cell types
  • Reprogramming of fibroblasts to iPSCs
  • Hematopoietic precursors and cell types






Retrieved from "https://vastdb.crg.eu/wiki/Special:VastDB"