Special

MmuINT0078020 @ mm9

Intron Retention

Gene
ENSMUSG00000020080 | Hkdc1
Description
hexokinase domain containing 1 [Source:MGI Symbol;Acc:MGI:2384910]
Coordinates
chr10:61858146-61861452:-
Coord C1 exon
chr10:61861333-61861452
Coord A exon
chr10:61858242-61861332
Coord C2 exon
chr10:61858146-61858241
Length
3091 bp
Sequences
Splice sites
5' ss Seq
AAGGTAAGA
5' ss Score
10.57
3' ss Seq
GTTCCCCTCCTTTGTTTCAGGGG
3' ss Score
10.96
Exon sequences
Seq C1 exon
CTCTTTGACCACATCGTACAGTGCATCGCTGACTTCCTGGACTACATGGGCCTCAAGGGCGCCCAGCTGCCTTTGGGCTTCACCTTCTCCTTCCCCTGCAGACAGACATGCATCGACAAG
Seq A exon
GTAAGAAGGCCCTGCCAGGCACACAGCCGGCCCAGCGGCTGCCCTCCCCCAGCGGCTGCCCTCCCCCAGCGGCTGCCCTCCCCAGCGGCTGCCCTTCCCCAGCGGCTGCCCTCCCCCAGGGCCATTTCAAGGTTCCTCTGTGTCTGTGCTCACTTTGGGTTTTGTTTCTGAGACAGGGTCTCCTGTATCCCAGGCAGGCCTCATTGAGACAGGGTTTCTCTGTGTAGCCCTGGCTGTCCTGGAACTCACTCTGTACACCAGGCTGGCCTGGAACTCAGAAATCCACCTGCTTCTGCCTCCCAAGTGCTGGGATTAAAGGCGTGTGCCACCACTGCCCAGCTTCAAATTCCTGATATAGGCAGGGATCACCATGAATTTCTGATCTTCCTGCTTCCACCTTCTGTGTCCTGGGGTAGCAGGCCTGCACCACCAAGCCCAGCACACGTCACGCTGAGGATGGGGCTCAGCATAAGACGTACACTAGACAAGCACTTTACTGACTGAGCCACATCACCAGGCCACTGTTCACACGTCTGGGAACACGTGGTGTAGAGGGAATTAACCATTTAAAGGGTTTTCTATACACCTGATTTCATATCTCCTTATTTTGAAATTCACAAAAAGAGTTAATTCCCTGGGTTTGAGAAGGAAGTGGTCAGCAAAGGCTAATTAGAACTGGGCAATATTTTTATGTCCTCCGAACAGCACATGTGATCAGGGAGATGTCAAAGTTGTAGGGTTTTTGATAGATAAAAGCTCACCCATGTAACTAAGAAATGTGTTTCTCAAGCTGTCCTGGTGTAGGGAGTTCAGCGCCAGCCTGGGTTACATGATACCCTGCCCTTCACCAGTGATGATGAGGAGGAGGAAGACAAGGGGGAAGAAGAGGAGGAGGAGGCTAGATACACCCACAGCATCCACGGTGCTACTTCTGTGCCAGACACTGCTTTGTGCTTTTCATGAGCTTTGCTTCAGGTTGGGGAAAAAAAAACCTAGCAACAACCACAGACCCTGGTGTGAATTGTCAGGCGTGTTCTCATTTATTGGCTGTGTGACCCTGGGTGCATTCTTTAACCTCTCTGTGGTTTTGTTTTCTTATTTTTTACAAATGAATCTAGGAGCTGTCAAGTTGAGTCCGAAGTTTACTGTTCTTGCAAAGGACTCAGGTTCCGTTCACAGCATGGTGGCTCATGGTCATCTGGAATTCCAGTCTCAGGGCATGTGACACCCTGTTGTGAAATTGATGCACAACACACACGTGGTGCACATAAACGCACACTCACACAGACTTAAAAAAATAAATACTTCTTCATAAAATGAGGGTAGAATACCTGTTTACTTTGTAGGTGTGTTTGTGGGTTTCCAAATTTCTGCACAATTATACATGACTCTTTTGCTCAGTGACAGGAGATAGCGGATCCACATTACCGATCTAGGCGGCTCTCCACAGTGTACCACTTAACAAGGAAAACAAATGGTGGTAATTTACACGAAATATAAATGTGTTTATTTCAAAGTACAAGCAGGCAGAAAAAAGGGTTTAGAGGGATTCTCCTTGGACTCATGGTAGCCGTTATTTTTCAGGGGACAGGGAACCTCAGGGGGTTCTATTTTTATCAGTAACATTTTAGTTTGTTTCTTTGTTTTTATTTTTTAAACTAATGCACTCACACTATTGCTGCCATTAAGAAGAAACAGACTAAGCCTAGTGATGGTGGACATGCCTTTATCTCTCTGGAGGTGGAGGCAGGAGGATCTCTGAGTTTGAATGAGTTTGAAGATAGCCTGGTCTACATGGAGAGTTCCAGGACAGCCAGGACTACATAGAGAAACCCTAGACAGACATGTGTGTATGTGTGTGTAGGTCTGGTGGCTGAGAGCCTCAGGTGAGACAGCGTCTAGCCAAAGGTTCTGTGGGCATCCTTCCTGGCCCTGCATCCTAACTTTGTCAGTTGCTCCCACTCCCAGCTTTCTAAGCTGGAGCACTGGCTAGAATCAACCCATGACCAGGCTAATAGCTCCTAAACGTTAAGATACTGCCATGAACGTTAAGTGTATTGATTTTAGAAAGTTTGGAAAAATGAAAATGCACTCGTAGCCTTGGATCCAAAGGTAGCCAGTCAGTCAGTCATCCCTCTGTATAGCCCAGGCTGACCTGGAACTCACTTTGTAGACCAGGCTGGCCTCGAACTCAGAAATCTGCCTGCCTCTGCCTCCCAAGTGCTGGGATTAAAGGCGTGCCATTTTTTAAAAAATTATTTATTTTATTTATAAGAACACACTGTTACAGATGGTTGTGAGCCACCATGTGGGTGCTGGGAACTGAACTCAGGACCTCTGGAAAAAGAATCAGTGCTCTTACTTGCTGAGCCATCTCTCTAGCCCCTTACCTATGTCATTGTAAAAACAAGTGGACTTGCACTGGATGGTGGTGGTGCACACCTTTAATCCCAGTGTTTGGGAGGCAGAGGCAGGTGAATATCTCTGAGTTTGAGGCCAGGCTGGTCTATAGAGTGAGTTTCAGGATGTCCAAGGCTATACAGAGAAACCCTGTCTTGAAAAACCAAAAAAACCAAAAAAAAAAAAAAAGTGGGTTTCTTCTTTACCTGTGTATTAATGGCTTTCATTTAAAAATGTGTGGCGAACAGTTTTCCAATGCTCCATGTTTCTTGACAGTGTGATGGTCCTGGTTTGTAATAGTATTGATGATGATGGATAAGACAATATGTCTTCTCAATACTGCTGAGGGCAGGGAATAGGTCGTTCTACTGTGTAACGGTGTTGAGTCTGACATTTTTAATTCAACCTCTTGAGAGCACCTCCATCCATCATGGGCTACTTTAGCAGTGGGATGCTCTGACCCCAGACTTTGATTCTGTGTAGCAGCAACAGGAACACACCAGAGTCCTGAAGACCGCGCAGAGCTGTGGAGAGCCCATCTGGCAGGAACCATGCTGGGATGATGAAGGCAAAAGCAGGCCAAGAACATACACGGTCTACCAGTGACCAGACTCAGTGCCTATGGGATCTGAGGTGCTCTGTCATTCGGAGAACGGCTGCCCAAGTGAAGTGTTCCCCTCCTTTGTTTCAG
Seq C2 exon
GGGACTCTAGTAGGGTGGACCAAAGGCTTCAAGGCCACCGACTGTGAAGGGGAGGACGTGGTGGACATGCTCAGAGAAGCCATCAAGAGGAGAAAC
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000020080-Hkdc1:NM_145419:12
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact





	

	
ORF disruption upon sequence inclusion





No structure available

		

			
Features


			

				
Disorder rate (Iupred):
  C1=0.000 A=NA C2=0.000
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
PF0034916=Hexokinase_1=FE(19.2=100)

							
A:
NA

							
C2:
PF0034916=Hexokinase_1=FE(15.3=100)

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000020277





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000020277f667A
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chr10:69250653-69257035 
ALTERNATIVE
HsaINT0076409
(HKDC1)
Human
(hg19)
chr10:71010409-71016791 
ALTERNATIVE
HsaINT0076409
(HKDC1)
Rat
(rn6)
chr4:113566711-113568611 
LOW PSI
RnoINT0070963
(Hk2)
Cow
(bosTau6)
chr28:25779340-25782313 
LOW PSI
BtaINT0072348
(HKDC1)
Chicken
(galGal4)
chr6:10450273-10451513 
ALTERNATIVE
GgaINT1014873
(HKDC1)
Chicken
(galGal3)
chr6:11960626-11961866 
GgaINT0044686
(E1BRU7_CHICK)
Zebrafish
(danRer10)
chr13:22892061-22892202 
LOW PSI
DreINT0078089
(hkdc1)
Fruitfly
(dm6)
No conservation detected




Primers PCR

	

		

			
Suggestions for RT-PCR validation

			

				
F: 
No suggested primer sequences

				
R: 
No suggested primer sequences

				
Band lengths: 

			

		

	





	
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"