Special

MmuINT0078773 @ mm9

Intron Retention

Gene
ENSMUSG00000022485 | Hoxc5
Description
homeobox C5 [Source:MGI Symbol;Acc:MGI:96196]
Coordinates
chr15:102844439-102847860:+
Coord C1 exon
chr15:102844439-102844966
Coord A exon
chr15:102844967-102845658
Coord C2 exon
chr15:102845659-102847860
Length
692 bp
Sequences
Splice sites
5' ss Seq
ACGGTAAAC
5' ss Score
5.88
3' ss Seq
TGGGGGAATTTATGTTCCAGAGA
3' ss Score
4.79
Exon sequences
Seq C1 exon
CCCTCAACTTCAAAGAGTCACAAATCACCCTTAATCAAAAAGGGTGCAGAAATTTTTTTTGGGCCCTCCCCGCCATGAGCTCCTACGTAGCCAATTCATTCTATAAGCAGAGCCCCAATATCCCTGCCTATAACATGCAAACTTGTGGGAACTATGGATCGGCCTCAGAGGTGCAGGCATCCAGGTACTGCTACGGCGGATTGGACTTAAGCATCACTTTCCCACCGCCTGCGCCTTCCAACTCTCTCCACGGGGTAGACATGGCTGCCAACCCCCGGGCTCACCCCGACCGCCCCGCCTGCAGCGCCGCGGCCGCTCCGGGACACGCTCTGGGCAGAGACGAAGCGGCTCCTCTGAACCCTGGGATGTACAGTCAGAAGGCGGCTCGCCCGGCGCTGGAGGAGCGAGCTAAGAGCAGTGGGGAGATCAAAGAGGAGCAGGCGCAGACAGGGCAGCCTGCCGGACTGAGCCAGCCACCGGCCCCGCCACAGATTTACCCGTGGATGACCAAACTGCACATGAGCCACG
Seq A exon
GTAAACTTTAGGACTTCATTTTGCGCGCTCGGGTCCGCCTGGGTTTTATAGGCCATGCGGGGCAAATAAAGAAAAAAAACCTGCGGCCATAAATTTTACGATCCAGGCATCAATGGCTCGTAAAACTGTCCACTAAAAGGCTTAGAGGCTGTGTGCGCCCAAATTTACGACGACATAATTGGATCATAGGAACAAAACGTGTATAAAAGGCAATATTCAATTTTGGGGGGAGAGGGAGGGAGTTAAAAAAATAGAGGGATCTGAAGGGTGAGGAGCATGGGGCTCCAGAGTGGGGATCCCCCCGCGGCTCCCTCCCTCCCTCCCCTGCGGAGCCGGCTCGGCCAGTGCTCGCGGCTCCGGAGGATTCCAGCGACTCGGGAGGGGCGGGAGGGGGGTCCCCGGTGCTCGGATCTCGAGGGTGCTTATTGTTCGGTCCGAGCCTGGGTCTCCCTCTTCCCCCCATCCCCCCTCAGCCCCTCCGGCCGCAGAGTGAAGGCGGCGGTGGAAAGTTTCCTGCCCAGGCGGAGGCGCTTCTCCCGGGACCGGGCCTGCCCGCCTGCGGCCCTTCTGGCCTGTCCCACCGCGCTCACCTCTACTCCCTCCGACCACGGGTGGGGCCTGGGACTAGGGTGGGACGTTGGAGTGCTGCACGCTATTCATCCCTCCCTGGTTTGGGGGAATTTATGTTCCAG
Seq C2 exon
AGACGGATGGCAAGCGGTCCCGAACCAGTTACACGCGCTACCAGACCCTGGAACTCGAGAAAGAATTCCATTTTAACCGCTACCTCACTCGCCGCAGGCGCATAGAGATTGCCAACAACTTGTGTCTCAACGAGAGACAGATCAAGATCTGGTTCCAGAACCGCAGGATGAAGTGGAAGAAAGATTCCAAAATGAAGAGCAAAGAAGCTCTTTAGAGGAAGCAGGGAGCCCTCAGAGAGCACCCCGGTCTGCTGTGGTCCCTGCGCCCTTCCTTTTCGGTTTTCCTCCTTCTAGATTTTGAGGCGGAGGCTAGAGCACTGGCTCCGGGCCTCCCAGACAAAAGCGCATTTCTTTGGCATTCCGAATCCCCATCGACCCAGGGTTCCGCAGGACCGCCTGCACTGCCTGTCTTGCCTCAGCTCAGCTGAGCACCCCAGGCCCGGGGCACATTCTTGTAGGGCGGGTACTGGATAAGTCTCAGCCTGGGCTGCCTCTCTCGGCTCCGAGCCCTAGTTCAGCTAGCCTGAGTTAAGGTGAGACAGACTGACTGTAACCCCTTCTCCCCGACCTCCGCCTCACCCTCTTCTTTGTTCCTGCCTAGGCTGACCAGCCTGCTGAAGGCTGGTTGTGCCAGGCAGAGGCTATGACTAGCTAGAATCGGGGTGCTTTCAACTAACCTTTGTAACTTCTAAACTGTCTTTGCTCATTAATTATTTGCATATGAAAGAGGGAGATAAGTGAAAGTGGGCCTGTAACCCCGGAGGTTGTCCTATGCTCTCTATACCTTCCAATCCCCTTCCCAAAGCCCGGGAACTTCCCTAGCCTGGCTTGCTGCATGCACTCTCAGGTTCACAGTTCCAGCCTGCTAGCTAGCTCAACTATTGGGGTCTCTTGTCTTTGGACCCTAGCAAGTTGTTCTTTGAGGCTTTTTGCTATCCTATATATCTTGCCATGACTTTCTCACCTTCCTGCCCCATTGCAGTTGCCCAACTATTTATTGACTCCAAGCCCTTCCTGAAACTATATTTTGTCATATCAAATAAAGCCAGAAAAAGAACAGGACTAAAGATTCAATTACTTCTGTCTGTTTAGGGCATGCATTGAATTGATGTGTCTAAATAGGCTCTGAGATGTATTGGGAGGCCCAGTCTTTAAACCATCCCTTAAAAAATATTTTTAAACACCTTTAGGAGCAGCAAGAATAGGGAACAATGGAACTGAGTTCTTTTCTTGATTCATGGTTCCAAGAAGGGCCTCTGGGGTGAAGGGGAGTACACTTGAGGACTCCTGTACTGTTGTTTCCACTTGCTGTGTGTGTCTAAGTTACCCAGACTTTTCTATATCCTATTCTCAACGTTGGCTAAAACAACTTGAGACTTGAAGCTTCTAGACTGTAGTCTGTACTTTATGCCAGAGAATAGTAGCTCTGTGGCTCCACTGACTTAGATTCAGGCTCTTCTGGGTCTAGGTCATCCTTGTAGGTCCTTTCTGACATAGAAGAAAGGTTGAGTCCTCTGTCTAGATGCCAGAAGGATTCGCAGCAATAGTAGGTGCTGCTTGGTAAAGAGGTGTTGGGGAAGGAGAAATGGCCACGGTTTGAGATGTTCTTCAGCCTTCTAAGATATGGGATGGGGCAAGGGGGACTAAGGAGACAGTGAATGCAACCTGCAGTGTGTGCCTGCCTTAGAGAAAACATACAGACTGCTCCCTGTCTTCTAGGGTCTAAGCCAATGAAGGACAGTTAACTGGAATAAGAGCTGTATAGATCAGTGTGGGAGCCATGCCTGTTTGCTGTCATCTATCATATCTCTGAGATTTTGTATACAGGGGGAGGGTGCCCTATAGGAGAGGGTATGCAGCTAATTCAGGTGGGGCTGGCCTAGGCTGATGCGCTGCTTAGCTCCACTCCAGGCTCCAGGACTTGTTGAAGGAGGAAGTACTTTACAGGAGAAACAAACGCACGGAATGGGCCCATAAAACCTTACTGCATTTCCTCTCCAGCCTTCCACAATGGGGTGATTTCCTGGAGCCAAGCCTAGGCCCCCCACACTGGAGGAGTGGGGAATCTGAAACTGGGCTAAGGGCTGCTCTACACTAGGACAGAAAGGAAACAGAGTGGCTCTGGGGAGGGGCAGGGAGATTCCTTTTTATGATTATTAATGCTTATGCTCTTTGAATTTATTAAAGGTCTGACTTCACTGC
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000022485-Hoxc5:NM_175730:1
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact





	

	
Alternative protein isoforms





No structure available

		

			
Features


			

				
Disorder rate (Iupred):
  C1=0.684 A=NA C2=0.282
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
NO

							
A:
NA

							
C2:
PF0004624=Homeobox=WD(100=79.2)

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000001709





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
NA
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
No conservation detected
Human
(hg19)
chr12:54427361-54428061 
HsaINT0077307
(HOXC5)
Rat
(rn6)
No conservation detected
Cow
(bosTau6)
chr5:26157646-26158342 
Chicken
(galGal4)
chrUn_AADN03012159:486-725 
Chicken
(galGal3)
chr2:32558583-32563159 
ALTERNATIVE
GgaINT0096338
(F1NMG1_CHICK)
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected




Primers PCR

	

		

			
Suggestions for RT-PCR validation

			

				
F: 
CTCCTCTGAACCCTGGGATGT

				
R: 
CACTTCATCCTGCGGTTCTGG

				
Band lengths: 
355-1047

			

		

	





	
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
  • 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"