Special

MmuINT0078141 @ mm9

Intron Retention

Gene
ENSMUSG00000066842 | Hmcn1
Description
hemicentin 1 [Source:MGI Symbol;Acc:MGI:2685047]
Coordinates
chr1:152527741-152530887:-
Coord C1 exon
chr1:152530720-152530887
Coord A exon
chr1:152527855-152530719
Coord C2 exon
chr1:152527741-152527854
Length
2865 bp
Sequences
Splice sites
5' ss Seq
CAGGTATTC
5' ss Score
6.49
3' ss Seq
CGGTGCTTTGCTTTTTCTAGGAG
3' ss Score
9.46
Exon sequences
Seq C1 exon
CCCCTCCAAGCATCATCGGGAACCACGGAGTCCCTGAGAACGTCAGTGTGGTGGAAAAGAGTTCTGTATCCCTGACCTGTGAAGCCTCCGGCATCCCCCTGCCTTCCATAACCTGGCTAAAGGATGGCTGGCCTGTCAACCTTGGCAGTTCTGTGAAAATTCTCTCAG
Seq A exon
GTATTCTCAATGGATAGTCTGAACATCTGGTTACCTTCCTGTAAATTTCGTTCCTCTTCTGTTTTTCATTTTACTGTTTAAGTTGCTTCAATTTCCTTCTGACCTAGGTACTTATTATGACACCTATTAATCATATTACACAACATATTTAAAACATAGAAAGTTATGTGAAAAGGAGTCAGCATCATCTTATTAGCAATGTTAGCAGCCCCCTTGTACTAACTGTCAGCAGGCGCATGACTAGTCTGAATGGTTTAATTTAATTTTTAAGAAGAGAGTTCCCGCTGGGGGTGGTGGCACAGATCTTTAATCCCAGCACTCAAGAGGCAGAGGCAGGCAGATTTCTGAGTTCAAGGACAGCCTGGTCTACAAAGTGAGTTCCAGGACAGCCAGGGCTATACAGAGAAACCCTGTCTCGAAAAACAGAAGAAGGAGGAGGAGGAGGAGGAAGAGGAGGAGGAGGAGGAGGAGGAAGAAGAGGAAGAGGAGGAGGAGGAAGAGGAAGAAGAAGAAGAGGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAAAAGAAGAGAGTTCCCTATATGCTGCGACCTTATTCCCAGCCCAGCTTCTGATAATTTTGTAGGGAAACCTATCTTATCCCACACGGGTATCAGTGGAATACTGGAGAGAGGGATTTTGAGGCATGTCACAGGAATCTACAATTGACCTAGTTTAATAATGGTGATCACATAGACTAAAAAGACAATCATTCTTTAGCTTTTGACAAAGTTATTCAACTTGGTTAACCTTGGCAGCATCCGTGTCCTGTGACATTCAAACTGAAGTGAGTTTATATCATGCTAAGCTATTAACACTGTGCTTGCTAAAGAATCTGATACTCATCCGGTATCCTGGGAAACTGCCTGCATCCTTCCTGTGTCCTATGAGCTTTTCATTTCATAGGACTCTATCTCTGCGGCCCTATAAAGAGAGAGAAGTGACAAAGCTTTTATTGCAGTCTGGCTACCAAAATCCTGAGCATGTTGTCTTCTTGCCTCAAAATTATCTTCATTTCTTAACAAAAATAGTTTCAGTTCCGTAAAGTTTGAATTTATTAAATGTGATAACATCAAAGATCTCAGAAATAAAAACAGCATGTCGGAGTGCAGTCGGCTGGCTCCCTCCACATTTACAGGAGTGGTGTTTGGTTCTACTTGGATTTGTTTTGATTGACCAGCAGCTGGAGATCTCTGAGCAAAGCACATTAAAAGTATTTCACCTTGTGACTGCCAAAGGACCCACTCAGCTCTACAATCTGGATGTGTTTAGTGTGATGGACAAATGAAAAACAGATGAGTGGCCTATGACCTGCACACTGCAGCTCTGCTGCAGACTTCTGGTCCATTAAGGCAAAGACTCCTGAGAATTGCCTGCAAGCGGGATGCTGGTGACCACCCTATCGTGGTCATAGAATTGCCCGTCAAGAACAGATAACTGCCATAAAATCCAGTAGTGACGAGAAATGGCTTCACATACGTATAAATTGCTAGCATACTCATTTCAGGTTTCCAAGAGAAAACCTTGTGAGAGGATCAGGGAACGGAGAGAAAAGAAAGATGATTGTGGACTCAGTAATGACTTATAAACGTTGTGTCACTTTAATACCCCTCAACTGGAACCGTATTGCAAACTCACTGATCTGAGCTGGCAGTGAATGAGCAAATCCTTTGAATCCTTTCAGAATTCACAGAAGTGTTTTTTTAAAAAACAAAACAAAACAAAAAATCTGATTATGTTGTTTACCTCTGTTCTGCTGGGGAAACAAAATTCAGTTCAGGAAATCTGCTTTGATTTCTTTTTCAAGTAAGATATTGCAAAAGTGACCTTCTGGTAAATTGAGAACAGAGAAGCTGCTGGTTAGACAAGTCTGATGTCAGCTTGTTGCTATAGAAACTGAAAGCAGATGGTAGCTTTTCAACAAGAGCCAGGTGAATATTTAAGTGAGAATTTTATGTGTATCCATTAGCCTTTTTTTAATACAAATTCAAGGTGCTAAACAAGAATATGCCTGCCCAAAAATTTATTGATAAATCTGAGTAGTGGCTTTTTCCCCCTGAGATTTTTTCATTCGGCGTTCTCGGCTTCCACTGTGTCTCTATACCTTTTCAAAAGGCTTTGCTTTGTCTTATTTGCTGACTCTTCCATCTTTGTCCTTAAACAACATTTCCTGCCAAGTTCCATCTTTTAGCACGTCTCTGTCTATATGCATTTCCTCTTCGAGCAAAACAGAAAATCAAAATATGGAACGAAGCCAAGGAAGGCACGGTAGCGCCCGTGCCTGGGGTGACGTCACCCTCTAACCCTGCCATTAATGACTGGGAGATTTCCAAGAAGCTGACCTGGCACCGGGTAGTTGGTCCATCTTCATGGTTTACCCTCCCGCTCGAGAGGATGTTATCCTATAGAGCCCTATTGCTGACACTCGAGTTTTATCTTCCAGCCACATTTCGCCATCTTTTCCTGAGCATCCGGTCAACGCCCATTTGTGGAAGCGCCAATCAGACTACGACCCTGTTTTATGCATTGCAGCTCCCTCCTTCACCTTCAGCAAACACTAAATTCCTTAGCATAACTTCCAAGGGCACACAAAACCTGGCGAAACTTTATCTGACTTCATCTGCCCTTTCTCACACCCATTTTGCTGTAGACAGTACTATCATCCCTGCCTTATAACTCAGTCGCTTCATACTTAGCAACAGCAGAATCTCCCCTTCTCAGCAAAACTCCATTTCTCACTTGATGTCACCTGGAACTGTATTAAAGTCATCCGGTGCTTTGCTTTTTCTAG
Seq C2 exon
GAGGCAGGATGCTGCGGTTGATGCAGACCAGACCAGAAGATGCTGGCCAATATACTTGTATTGTAAGGAATGCAGCTGGTGAAGACAGGAAAATGTTTGGACTTTCAGTATTAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000066842-Hmcn1:NM_001024720:46
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:
PF0767911=I-set=PU(56.5=84.2)

							
A:
NA

							
C2:
PF0767911=I-set=PD(42.4=92.3)

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000074340





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000121500
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chr1:186057402-186061850 
LOW PSI
HsaINT0076610
(HMCN1)
Human
(hg19)
chr1:186026534-186030982 
LOW PSI
HsaINT0076610
(HMCN1)
Rat
(rn6)
chr13:68032767-68035126 
LOW PSI
RnoINT0071139
(Hmcn1)
Cow
(bosTau6)
chr16:68562604-68567041 
LOW PSI
BtaINT0072492
(HMCN1)
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
chr8_random:311302-314191 
ALTERNATIVE
GgaINT0000476
(HMCN1)
Zebrafish
(danRer10)
chr20:34294264-34296240 
LOW PSI
DreINT0078235
(hmcn1)
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"