Special

MmuINT0037265 @ mm9

Intron Retention

Gene
ENSMUSG00000029915 | Clec5a
Description
C-type lectin domain family 5, member a [Source:MGI Symbol;Acc:MGI:1345151]
Coordinates
chr6:40532234-40535247:-
Coord C1 exon
chr6:40535149-40535247
Coord A exon
chr6:40532294-40535148
Coord C2 exon
chr6:40532234-40532293
Length
2855 bp
Sequences
Splice sites
5' ss Seq
ATTGTGAGT
5' ss Score
7.35
3' ss Seq
AGGATTTCTTTTCATTTCAGTCT
3' ss Score
6.1
Exon sequences
Seq C1 exon
ATCCCTGAATCCCCATCATCATGAACTGGCACATGATCATCTCGGGGCTTATCGTAGTAGTGATCAAAGTTGTTGGAATGACCTTTTTTCTGCTGTATT
Seq A exon
GTGAGTATTTGCGGAAGCCCTCCCACCAACCCCAGCATCTTTGTTGTTTTATTCTACTCAGAATGCCAGATTGAGTGTAAAGGTTCAGTGCCCAAGTTCTTCCACATTGTCTTCCCATACTCTAGCAGACACATGGGATCAGGTTCCATGATCTACAATGGAGACACACAACTGACTATAAAAATAAGAGTCTTCACTGGATAATCTAAACTGGAGTATTTAGCCTGACTTTTTTATTGTTGCTATAATTTTAAAAATTACTCTTCTAGTTCAACCCAATAAAGCTGTATGAAGAGCTAACTATAAGAGCAAGATTTAACAGAGGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTTGTACATAAATTCTTCTCAATAAATTCATTAGTACAGGGAGCCTCGTAGCCAAAGATTTAGTTCTGAAGCCAGTAGGAAAAACTGGAGGAAGGAAATGTGGGTAAATTGCAGCAGTTGGGTAAGAGGGATTTTCCTTGTGACCCAATGTGAACATGTAATAACTATAACGGGCTCAGAAAAGATACACAAGTAGGTAAGGGAAGGGTGAATATACACACACCTCACGGAGGCAGAGCTCAGTGCTTCCTCCTGTGGTCACAGTTTCCTGGCATCCCCTGAGGCTCATTTACTGCCTTCATTTGCAGCCACACTGGAACTGAGCCACTAGCTGGTTTTCTTTGCAGTCCCACAGGTTTTTGGCAAAAGTAATGATGGCTTCGTCCCCACGGAGAGCTACGGAACCACTAGTGTGCAGAATGGTAATCTCACTAGCATCCAGCTTCTATGTCCTGAATTCTAACAGTTCCTATGAATTTGTATACAGATGCTACACCAAGGTCCTGTTCTCCTTTACAAGTGTGAAAATGAACAGAAAACTCATTGATCACTGTATCTTCCTGATTTTTCCTCTATTGGTACTAAGGATCAAATTCAGGGCCTTGCTCATAGGAAGCACAAAGTCTAGTACTGAACTACACCCACCTCAACCCCTGTATGGAATTTATGATCCTCAGTTTTCCTCCTGGGCTTGAGAACGATTTGTGTGGGACTACTATAATATATTGTAAGTGAATTTCATGGATTCTTACAAGGAATTGTTACAAACAAAATTCTATCCAGGTGTGGTGGCCCAAACCTTTAATCCCAGCACTCAAGAGGCGAAGGCAGGTAGATCTCTGAGTTTAAGGCCAGCCTGGTCTAAAGAGTGAGTTCCGCTGGGAGTGGTGGCGCAGGCCTTTAATCCCAGCACTCGGGAGGCAGAGGCAGGCGGATTTCTGAGTTCGAGGCCAGCCTGGTCTACAAAGTAAGTTCCAGGACAGCCAGGGCTACACAGAGAAACCCTGTCTGGAAAATAGAAAAGAAACAAAATTCTAGCATTAGAAGATGGTTCACCTGGTAAAGTGAATACTTGAATGAGGACCTGAGCATATATCTCCAGCACACAAGTGAAAGTCAAGTCTTTGCCATGTGTGTCTGTAACAGCAAGACTGGTGGATGGAGACAGAGCTGGGAGAATCCCTGGTACTCGTTGGCCAGTCCGTGTAGTTGAATTAATGAACTCCAGTTTCATAAAGAGATCCTGCCTTAATACATGAGATGGACAAAGATTGAAGAAGGCACCCAGTGTCAGTCACTGGTCCCCTCACACATGAATGTAAACACATCTTCACACACATGTACATACATCCACTCAGGCATGTACATACAATGCATACACACAAACACATGCACATACATGCTCACACACAGACACAAACACACACACACACACACAGAGACACACACACACACACAAAAGAATTCATGTTCCACAAAAAAAGGGGGGCTAGGCATCATTTTGTGAACTAAAAATTATGCTAGACTCACCATGGGATAAGAATAAAAACAGATTGGTAATCAAGCCTCATTTATAACACAAAAAATTTAATGCCACATGTTTCACATACAGAGGCCATGGGACTTCTAATCCTACCTCTCTTCTATTTGATTTATTCATTTTTATGTGTGTGAATGATTTATCCTCATGTATATATGTGCACCATGTGCATGGGCTGCCTATGGTTGCCAGGACACTGTATCCTCTGGAACCAAAGTTACAAGTGTTGTGAGCCAACATGGGGATGCTGGGAACTATGCCATCGCTCCAGCCCCAAGCCCACTCTTCATGCAGCTTTCTGCAAGGACTCCCTGCCACTGCCTCTTAAGACATGGGCTACAATTGACATCTTTAGGACCAAAGAAGAAATTTCTAACTTATCAAAAATGGACTATTATGATATCAAAGTCTCTGAGCTAAGGAGTACAATAAAATATGAATGCTCATGCCTGTTTTAACAATAAGAGTTTAAGTGACTAGTTGGCATCTGGGTAAATGAAAGTAGTCTTAAGCATAAAGAACAAATAACCAGGGCCCCTGAGCAGACTTTCAATAGCCTGTGGAGCCACTGAAACTGTCTGCTCAGACAGCTGGTGCATCCAAGAGAAAGGAGCCCCTTAGGGGCCATTAATCTCCACAGTTTGTATTTTAAAGACAGTATTTTTGACAATTCTAGTTCAGAGTGGTCAAGGCCCTTTTCCTCTCCATAGTATCTCTTTCAGCTTCTTCTTCTCTTCTTCCCTCCTTCTTTCTGCACCTTCCCATCTCAAATTTCCCTGCCCCAAATAGGATTTTCATCAAGGATAGTGTTTTTTCTTTCTACCTCTGGATCGTCTAGAATATCAGGGGTGTTTAGAAACAAATACTCAAAATTCAGCAGCCCACAGCCTAATGACTGCTGTGTTCACTATATAGTAGCCATCAGGATTTCTTTTCATTTCAG
Seq C2 exon
TCTCACAGATCTTTGGGAGAAATGACGAAAGTACCATGCCTACAAGGAGCTATGGAACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000029915-Clec5a:NM_021364:2
Average complexity
IR-C
Mappability confidence:
NA
Protein Impact





	

	
ORF disruption upon sequence inclusion (1st CDS intron)





No structure available

		

			
Features


			

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

				
Domain overlap (PFAM):

					





						

							
C1:
NO

							
A:
NA

							
C2:
NO

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000099030





     
      









    
Other Inclusion Isoforms:
ENSMUSP00000121848
          









    
Other Skipping Isoforms:
ENSMUSP00000135240
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chr7:141945401-141946213 
ALTERNATIVE
HsaINT1007825
(CLEC5A)
Human
(hg19)
chr7:141643765-141646013 
HsaINT0036269
(CLEC5A)
Rat
(rn6)
chr4:68818506-68819231 
LOW PSI
RnoINT0037231
(Clec5a)
Cow
(bosTau6)
chr4:106067012-106070302 
BtaINT0039232
(CLEC5A)
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
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






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