Special

MmuINT0078140 @ mm9

Intron Retention

Gene
ENSMUSG00000066842 | Hmcn1
Description
hemicentin 1 [Source:MGI Symbol;Acc:MGI:2685047]
Coordinates
chr1:152530720-152534076:-
Coord C1 exon
chr1:152533795-152534076
Coord A exon
chr1:152530888-152533794
Coord C2 exon
chr1:152530720-152530887
Length
2907 bp
Sequences
Splice sites
5' ss Seq
ATGGTGAGT
5' ss Score
10.13
3' ss Seq
ACTTTGGCTTTGTCTTACAGCCC
3' ss Score
9.68
Exon sequences
Seq C1 exon
TCCGACCATCAATAACCAACAGTGGTGGCCACCGCCCTGAGATTACTGTCATCCGTGGGAAAAGTATTTCTTTGGAATGTGAGGTGCAGGGTATTCCTCAGCCAACAGTGACCTGGATGAAAGATGGCCGCCCCTTGACCAAGGGAAAAGGAGTGGAAATATTGGATGAAGGCCGAATCCTTCAGCTGAAGAATGTTCATGTGTCTGACACCGGCCGTTATGTGTGTGTTGCTGTGAATGTAGCAGGAATGACTGACAAGAGATACGACTTAAGTGTTCATG
Seq A exon
GTGAGTAGAAAGAGAAGCAACCAGATCAATCACAGGATAAGGCAATCCAGTATCCTGGGAGCATAGACCTCTGAGCTGAAAGTCTTACATTCATATCCTAATGGCTTTGAAGTTCTTTGAGAGCTTCATGAATATATATAGTGAAATATGATCATTTAAACATCCCATCCTTCATTTTCCCTCCAAATCTACTCATATCTCCTCCAGTACCTTTCATTTCAATTTATTATTTTATCATCATATCATCATTTTTATTCTTTTTCTTCTCCTCCTTTGTCTTCTTTTTAAATACTCTTTTAAATACATTTTATTTTTTACTTGTTCACTTTACATCCCATTCCCTGGCCTCCTTCCAGTCACCCCTCCCATATTCCTTCCCTTATCCCTACTCCCCCTCTCTACTTGCAGATGTCCCCTCTGGGTATCCCCCCACCCTGGCACTTCTAGTCTCTGAGAGGCTAGGCACTTCCTCTCTCACTCAAGCCAGACTAGGCAGCCCAGCTAGAAGAACATATCCCACATGCAGCCAACAGCTTTCGGGATAGCCCCCACTCCAGTTGTTAGGGATCCACAGGAAGAACAAGCTGCACATCTGCTACATGTCTGCTGGATGGTCTAAGTGTATGATCTTTGGTTGGTGGTTCAGATTCAGAGCCAGGTTAGTTGACTCTTTTGGACTTTCTGTGGAGTTCCTATCCTCTTCAGGACCTGCAGTCTTTCCTCCTATTCATCTATAAGAGCCCTAATCTCTGTTCACTGTTTGGCTGTAACTATCTGAGCCAGCTTCTGGGTAAAGTCTCTCAGAGGGACAACATGCTCCTGCTTGTAAGTCCTTCTTCTCCTCTTCTTTTTTCTCCTCCTCTTTCTCCTCCTCCTTCTCATTTTTCTTCTTCATAAATTACTAAGTCCAAATAGCACTGCCCATATGTGCATGGTATGAAACCATGAAGCACTGGAAAATTTCTAGTTGGCCACGTCCTCCAAGAGAATGATTCTCCCTTCTCCAGCAGCTCTTAACTACCAAGAGCTTCTTAATAAGGCATAGGGTCTAGAGTTATCTCCCCCATTTATGCATGAATTTTGACTGGCTTCATCTTGTATGGCAAGCTCTTATGCAGATTTGTACAATGTGAGATCATGAGTGTAAGAAGACAGTGTTCTATCCCATTTCTAAGTATTTATGACTTCCCTAGTCACATCATTATCTTTCCATGTCTGACTTCATGGTACTTGCTGAGACGAACACATATTCGGTGTTCTTTTGAGGATGTATAGAATAAAGTAGACAAAAATCAAGGCAAGCAATCACAGTATAATTGGCTGACCTGGAACGCACTGTGTAGACACACCAGGGTGACATCAATCAACCTGCCTCTGCCTCACCAGTGCTGGGGCTAAACACATGCACGACAAGCACCACATCTGGCTGCATCTTTAATTATAGAATTTTCAAATTCAAATCTTAAATAAAGACTATTTAACAGTCCCATGGGTATGAGGTATATCTATTAAAGTCAGATTTAAGATTCTAATGAGTAAATGACAAATTTGGTTCAGGAAGAGGCTAAATATATGCCTATTGAAAGTCAACTATTTGCACGCATGCAATCTGATGTATAAATTTAAAATTTATAGAAGCAATGGGGAATCTAAATAGAAACAAATCTTAGAGCTTGAATCCCATAAATAAATGAATAAAGCTAGGTCTACTGGTGCATATTTATAATCCCAGTACTTTTTGAGGCTGTGTTTGGAGGACTGAGTTCAAATCCAGCCTGCCTCCATAGAGAGTTCCAGAGCAGCATTATTTACAAAACCAAGTTGTCTCATAACACACCAAAAGGAGAAGAATAAAGCTTAGTGGTAATCTCTTACATTTGTGACCAGCATGTATGCCAAAGATGAAGGGAGCATAAAAAGAGAGATAATTATTATATTCTTGTTATATTATTTTAATTTTTAAGATTATAACTATTCTTCATTAATTTATTTGATTCACTTTACATCACTGCCTCCTTCCTCCTCTCCTCCCAGTCCCACCCTGACAAATCCCTAACCCCATTACTCCCTCCTCTTCTCCTCAGAGAAGGGGAAGCCCCACATGGGTACCAACCCACCCTGGGACATCTAGGCTCAACAGGACTAAGCTCATCCTCTCCCACTGAGGCCAGACAAGGAAGCCCAGTTGGGGAAGGGAATCCAAAGGCAGGCAACAGAGTCAGAGACCAAGGTGCACATCTGCTACAAATGTGTAAGGGGTCTAGGTCCAGTCCATGCAGGGTCTTTGGTTGATGATTTAGTCTCTGTGAGCCCCCATGGGCCCACAAAGCATACTGTCAGGGATTGGCTCTCACACATGGGATGGGTCTCAAGTTGGGCCAGTCATTGGTTGGCTATTCCTTCAATCTCTGCTCCATCTTTATCCCTGCACACCTTGTAGGCAGGACAAATTTTGAGTCAAAGCTTTTGTGCGTGAATTGATGCCCCCCACCCTCCATTTGAAGTCTTATCTGGCTATAAGAGGTGACAACTTCAGGCTCCATATTCCCCTCCCCCCATATACTCCCAGGAACCTCTCCATTCCCAGATCTCCAGTTCACCCCAGAGATGCCCCAACCCACTGATTTCCATTCAGAATCCTGTCTCTAAGAAGGCTGTGAATCTAAATTATAAATCTGTCAGAAAATATGACAAACTCAGAAACTAGCTTACCATTGCTGAGCTATCAATGAATTCAAATTGGGAAGCAGTGACATATATTTTTATCTTCAGAGTTAGCATTGTTATGGTTCCTTATTTTGAGTACTATTAACCAGAAAATGGATGGTTCCTGATAGAAATAAGCTGTTGAGGATTAGTGTTTATTTCTTACTTTTTATTTCCAGTCACTTTGGCTTTGTCTTACAG
Seq C2 exon
CCCCTCCAAGCATCATCGGGAACCACGGAGTCCCTGAGAACGTCAGTGTGGTGGAAAAGAGTTCTGTATCCCTGACCTGTGAAGCCTCCGGCATCCCCCTGCCTTCCATAACCTGGCTAAAGGATGGCTGGCCTGTCAACCTTGGCAGTTCTGTGAAAATTCTCTCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000066842-Hmcn1:NM_001024720:45
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact





	

	
ORF disruption upon sequence inclusion





No structure available

		

			
Features


			

				
Disorder rate (Iupred):
  C1=0.042 A=NA C2=0.000
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
PF0767911=I-set=WD(100=88.4)

							
A:
NA

							
C2:
PF0767911=I-set=PU(56.5=84.2)

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000074340





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000121500
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chr1:186055675-186057233 
LOW PSI
HsaINT0076609
(HMCN1)
Human
(hg19)
chr1:186024807-186026365 
LOW PSI
HsaINT0076609
(HMCN1)
Rat
(rn6)
chr13:68035295-68038458 
ALTERNATIVE
RnoINT0071138
(Hmcn1)
Cow
(bosTau6)
chr16:68560778-68562435 
LOW PSI
BtaINT0072491
(HMCN1)
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
chr8_random:309649-311133 
ALTERNATIVE
GgaINT0000475
(HMCN1)
Zebrafish
(danRer10)
chr20:34296409-34297491 
LOW PSI
DreINT0078234
(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"