Special

MmuINT0078779 @ mm9

Intron Retention

Gene
ENSMUSG00000050368 | Hoxd10
Description
homeobox D10 [Source:MGI Symbol;Acc:MGI:96202]
Coordinates
chr2:74530005-74533159:+
Coord C1 exon
chr2:74530005-74530781
Coord A exon
chr2:74530782-74532147
Coord C2 exon
chr2:74532148-74533159
Length
1366 bp
Sequences
Splice sites
5' ss Seq
AAGGTCGGT
5' ss Score
7.13
3' ss Seq
TCTCCCTTTAATTTTGTTAGAGG
3' ss Score
4.45
Exon sequences
Seq C1 exon
CACAATCTCTCTTCTTCAAATTCCTCCCCAAAATGTCCTTTCCCAACAGCTCTCCTGCTGCTAATACTTTTTTAGTAGATTCCTTGATCAGTGCCTGCAGGAGTGACAGTTTTTATTCGAGCAGCGCCAGCATGTACATGCCACCACCTAGCGCAGACATGGGGACCTATGGAATGCAAACCTGTGGACTGCTCCCGTCTTTGGCCAAAAGAGAAGTGAACCACCAAAATATGGGTATGAATGTACATCCTTATATACCTCAAGTAGACAGTTGGACAGACCCGAACAGATCTTGTCGAATAGAGCAACCTGTTACACAGCAAGTCCCCACTTGCTCATTCACCGCCAACATTAAAGAAGAATCCAATTGCTGCATGTATTCTGATAAGCGCAACAAACTCATTTCTGCCGAGGTCCCTTCGTACCAGAGGCTGGTCCCCGAGTCTTGTCCTGTTGAGAACCCCGAGGTTCCTGTCCCTGGATATTTTAGACTGAGTCAGACCTACGCCACCGGGAAAACCCAAGAGTACAATAACAGCCCCGAAGGCAGCTCCACTGTCATGCTCCAGCTCAACCCTCGTGGCGCGGCCAAGCCGCAGCTCTCGGCTGCCCAGCTGCAGATGGAAAAGAAGATGAACGAAAGCGCGAGCGGCCAGGAGCCCACTAAAGTCTCCCAAGTGGAGAGCCCCGAGGCCAAAGGCGGCCTTCCAGAAGACAGGAGCTGCCTGGCTGAGGTTTCCGTGTCCAGTCCCGAAGTGCAGGAGAAGGAAAGCAAAG
Seq A exon
GTCGGTATGAACAGAGTTGCCACCCCAGCGGGGCGTGCAGTCCGGTAAAACCTCGAAAAGGGAGCGCTCGGGTGCCCAGAGCAGAGCCCGGGCAGCGGAGCCCAGAGCCCATACTCCGCAGGTGCTGCTCCACCCGGCTTTTAGAAGGGATATCCCTGCCTTGAAAGGGTCGGGGCTTCTCTCCCGCTGCTCCGGCCAGACCTGGCCCCAAGCTGATGGCGCCTGGGCAGAGGACAGGCTTGCCGGGTTTATCAGTCTTGAGCCAGATCCGAAATACAACAAAAGAGCTAAAAGGAGACCAGCCGTTTGTAAACAGGGCTCCAGTGCCCGCTTTTCTTTGGCTCAGATTTGCAGCCCTAGTTTTTGCCTTGAACCCAGGGATCATTTTAAGGTAGCCTAAGACACCGTGTTTGTGTTCAAGGGTTTGCACCCCGCATCCTGCGATCTAAGAGGGAAAGGAAATGGTTTGGCCTGTTGGTGCTTGGGTGGGGAAGCAGAGGTAACCTTGGCTTTGTCTGGCGAAAGTGCCGCAGGCTTTGCAATCTTCTACAAAGGGGGCAAAGGCGGAGGAGGGGGAGAACAGATCTGCATTGCCCACCTAGGGCTGGGGTAATGCAAAGAACCAGGGATATGGGTTTCTAAGAAGGAATCTTGAGCCCCCACGCCCATTTCTGCAGTCTGTCCCTCACTGTCTACCGGGTGAGCCACAGAGTTACATTTCTGGAGGAAGGCTTTTGTGTGAGAGCAAAGAAAAATTGAGGAAATTCTGGGGGGAAGGGGGGAACTGTAACAATGCCCAGTCAGGGTGGAGAAGGGATCCCTGCTTCCTCATTATCTCTTGAAACAGCCTGCATCCCTATAAACCTGGTTGTGGATCTCCTTGTCTGCCTAGGAGGGGTGGGTAAGAAGCGGCCGACTTGGGGCCCTGGAGCAGTAGTGAGATACTGGTAGATGAAGCAAGCTATGGTTCTTTCTGGTGGCCTGACGGCTTAGAATGTTTTTGGGGGGACGGAGGAATCCTGTAAAGTTTGCTATTATAGTCACATTTTGTGCAAGCCAGAAAAGTTGTGTAGGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAATATGAGGAGGCAGCCTCTGGCACAGAATATCCTTTCATTCATCGTGTTAAGTATTTAGTTCTAAATTGGTACCAATTTACAATCCCCTTCATGCCCACCTTCGTAAGTGATGTTTAATACCAGCATTGTCCAAAGCAGCCCATCTGGCAGCAGGGTCATGGCCAAGGGTATATTTGAATGGACTGAGAGAAAAAAAAATTCTTGATTTTTTTTTCTTCTCCCTTTAATTTTGTTAG
Seq C2 exon
AGGAAATCAAGTCTGATACTCCAACCAGCAATTGGCTCACTGCAAAGAGTGGCAGAAAGAAGAGGTGCCCTTACACCAAGCACCAAACGCTGGAATTGGAAAAAGAGTTCTTGTTCAATATGTACCTCACCCGCGAGCGCCGCCTAGAGATCAGTAAGAGCGTTAACCTCACCGACAGGCAGGTCAAGATTTGGTTTCAAAACCGCCGAATGAAACTCAAGAAGATGAGCCGAGAGAATCGAATCCGAGAACTGACCGCCAACCTCACCTTTTCTTAGGTCTGAGGCCCATGTGAGGCCAGGATCCGAGAGGGGGCACCGAGTTCCAGGCCTGAGTGCTGGAGGACTGGCAAGGCGGAAACAAACCCTTCATTGCTCTTTGGTTTTTTTGTTTTGTTTTGTTCTGTTCTGTTCTGTTTTCCTGCTAGAATGTGACTTTGGGGTCATTCTGTTCGTGCTGCAAGTGATCTGTAATCCCTATGAGTATACATATATATATATATTAAAAAAACTTAGCACGTGTAATTTATTTTTTTTCATCGTAATGCAGGGTAACTATTACTGCGCATTTTCATTTGGGTCTTAACTTATTGGAACTGTAGAACATCCATCTAAACGTATCCATCGCATCCCACCCATCTATCCCGCCAGCAATGTGACTTTTCCATGTTTTTCCTAACATAAAAGTTCTCTGTGTGTGGTTAGCCCATGAACTCATGGCATTTTGAAAACATCCAGTATTTAAAAAAACAAACAACCTATATCTATATATATTTCAAAAGATTAAGAAAACCCACAAGCTTTGGGGGGAGGGGGACTTTAAAAAGCACATTACAATGTATCTTTTCACAAATGAACTTAGCAATTGTCCTTGGTGAAATGGAATATTGATGACTTATGCCTTGTAGCCTTTCCTTGTGGTGCATCTGTGGTTTGGTAGAAGTACAAGCGCAACCTGTGCTTTTCTGTGCATGTTCTGGTCGCATGTGTAATGCAATAAACTCTGGAAATGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000050368-Hoxd10:NM_013554:1
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact





	

	
Alternative protein isoforms





No structure available

		

			
Features


			

				
Disorder rate (Iupred):
  C1=0.510 A=NA C2=0.293
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
NO

							
A:
NA

							
C2:
PF0004624=Homeobox=WD(100=61.3)

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000062412





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
NA
  



Associated events







Conservation


Human
(hg38)
chr2:176117579-176118953 
ALTERNATIVE
HsaINT0077312
(HOXD10)
Human
(hg19)
chr2:176982307-176983681 
ALTERNATIVE
HsaINT0077312
(HOXD10)
Rat
(rn6)
chr3:61614978-61616339 
ALTERNATIVE
RnoINT0071664
(Hoxd10)
Cow
(bosTau6)
chr2:20829901-20831256 
ALTERNATIVE
BtaINT0073195
(HOXD10)
Chicken
(galGal4)
chr7:15804339-15805695 
Chicken
(galGal3)
chr7:17415879-17416027 
HIGH PSI
GgaINT0047471
(F1NZJ4_CHICK)
Zebrafish
(danRer10)
chr9:1967698-1968412 
LOW PSI
DreINT0078840
(hoxd10a)
Fruitfly
(dm6)
No conservation detected




Primers PCR

	

		

			
Suggestions for RT-PCR validation

			

				
F: 
CTTCCAGAAGACAGGAGCTGC

				
R: 
AAGAAAAGGTGAGGTTGGCGG

				
Band lengths: 
349-1715

			

		

	





	
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






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