Special

MmuINT0037161 @ mm9

Intron Retention

Gene
ENSMUSG00000033082 | Clec1a
Description
C-type lectin domain family 1, member a [Source:MGI Symbol;Acc:MGI:2444151]
Coordinates
chr6:129382140-129385311:-
Coord C1 exon
chr6:129385135-129385311
Coord A exon
chr6:129382292-129385134
Coord C2 exon
chr6:129382140-129382291
Length
2843 bp
Sequences
Splice sites
5' ss Seq
GAGGTGAGC
5' ss Score
8.7
3' ss Seq
TGTTCTTTTTTTCTTCCAAGGAC
3' ss Score
9.27
Exon sequences
Seq C1 exon
TTTTTCAGTTCTACCAGCTGTCTAATATCCAGCAAGACAGCATCACTGAAAAGGATGAAAAGCTGGGGAACATGTCCCGACAGCTACAGTCTCTCCAGGCCCAGAACAGAAAACTCATTGAAACTCTACAGCAGGTAGCCGTAAAACTGTGCCGTGAACTTTACAACAAAAGTGGAG
Seq A exon
GTGAGCATGTCCCTGTCACTCTGGCCTCTAGAAATTGTTCTATCTAAACCCGAATTTCCCATCAGGGTAACTAGAATCGTGTATTTCTTTAGAAGTACTTTTCCTGACATCTCAATAAACAGTTTGAGCTGCATAATCATGGTCAGACATTGGGTTATAATTGCTTATATGCATCTTTATCATGGTGCAGGAAGGGATTCTTCAAATGTGAGCACTTAAAGCATAGTAGTCCATTTAGAGTAACCAGAATAGCACCATCAGCAACTAAACACAGGACTATGCCTCAGTTACCTTGACACAGAGTAATCCAGCACAGGGAAAAAGTTATAACTACAATTTTCAAACTTTTAGACTCACTCAGGAATTATTTCAAAATTTAGAAAACCTAAAATAAATTACAGTTGTTTTAGTTCACTCATGGCGTGTTTCTCAAAAATATGTATCTTACAAAGGATCAAGGGTAATGAGAATGACAATGGGCAAACCAAAGCTATCACTGATGATAACTGTAAACTCACTTCAGTGTCCCCTTAAACAGCCACCATCTTTCTATTCCCCTCTTGAAAGTCGCATCACAGTATACTACATTCACGTCAGCCCTCTCTTCGTCCCCCTCCACCACACAAGCATAGGAAACAACCTGCAGTTCGCAGTCCTAACTGGTTTCTCTTTTGGAAACTGAAGTACCACAATTTCATCATCTCCTCCCACACCACTTCCCCATTAGCAGATGAGTGAGTGATTTTCTCAGTAAACAGTGTCTCAAGGCTTACTTCTCTAAGTGATTGTTTTCCACATGACTAGAGACTTCATTTACTCTAATTCTCTCTTTTCTTGTTTCCCTGACAACCCAGTGGACTTTTCTTTCTCTTTGTCGGATTCTAAATCATCAAAGAAATAATTCTCATCTAGGTGGCTCAAAACAAAACAAAACAAAATAAAAACAAAAACAAAAACAAAAGGCAAGTGAGAAAAAATGTATGCAAATAAACTATAAACAATTTAAATATAAAGAGATATAAAAAGGTAGAAACTAGGAATGAGTGATCTAATCTGTGAGTTCAATATGTAAGAAAGTCTGGGTCACAAATATAAACAAATATTCTATATACCCATAATCTATTGAAAAAAACTAATAAAAAATGACCATGTATTTTTGGATGATGAAGTTTTCCTGCATCATTAAAATAATTGATCTGCCTTAGTGTGTTGCCTTGCTGAACCTTTTTGCTGCATTGACCATGTTGTAGCTATTGTCACATGAAGCTTCCCACACCGACAGAGACTTTATAGGAGGAGCTCACAGGAAATCAGCCATGTTCAGCTTGGGAACTCTACGGCCAGTGTTTCACTAGCTCTACATGTCAAAAGAAAAATATCTGGAAGCAATACTTTTTCCTGGCACATTTTCATCTCGCTGATCAAAAGTATACATCTCCCCTGAAACACATCCACATCGTCCACATTTACATGCATGTACTTATACCATTCATGGATGTGCTGTGTCCTGGGGAAATTTTATTTTTATCACAGGGTCATTTAGTAAATTCCTGTCTCAAAGCAAAAGTTAACAGAAAGCATGATCTATGTGGCTCAATCTGTAGCCTAGAGTAAACTGTGTTCAAATCTCCATCCCCTCCAGAATAAAATAGTGGTGCAAGCACACACACACACACACACACACATACACACACATACACACACACACACATACACACACACATACACACACACACACACACACACACAGACTTAGATGTAGGTTCCTGACTCTCAGGCCAAAGTCCAGACACCCATACCATCATATTCATGACACTACTACTCATCCATGTAAAATGTACAAATGTACATATGTGTTTCATCTTACTCTCAGCCCTTTGTACTTTTTTGTTTGGTTTGGAAGTGCCCACTGTCTCTCAACACACACATAACTTATACAGCATGGGTACAAGGGACTTACATCTGAAAACACCTGACAGACAGCTTCAAGAGGGGGAAGATTAACTTAGGTTCCAGCTTCAGACATGTCAGCTTACAATGGTGGTGAAGGCCACTGTGGGGCAGCTTCCACCAGGCCATCCTTGAGGCTAAGAAAAGAGTATGCACAAAAAGTGCTATGTGTGATGCAGCCCCAGTGACCAACTTCTCACTTAGCCGCTATTTCATCACTTGACATTAAAGCCTTCAGATTCAGAACCAATCAAGGAATCAGTCCATCAATGGTATCAAAGACATCTAGATCAATCATATGCTCAAAGCTCACCAGCTCAAAATTATGTCCCCAATGCTTATGAACCCACAGGGAGAATTTCATATCCGAATCATAGCATAGTCCTATGAACCACCTCATGAAGGGATATTCTGTCCACATTCTGCATAGCATAGGCAAGGAGGTTTTAGTCATTCATCATCAGATCCAACACTGCATGTAAATACTATCTGTTTCAATTTTTACTGAATGTTCTGCTTCGATCATAGGTCATTCTTGGTGTGGAGTGAGTAGCACAGTTGCTCACTCAAATATCTGAGACATATAAGTTACTTCTTGGAATGTTAAACACTGTTTATTTCCAAAAGTGGAAACATCAGATCCATGCAGAAGGGGTTGGAAAGATGGCTCAGCAGTTAAGAGCACTGAGTGCTCTTTCAAGGGTCCTAAGTTCAAATCCCAGCAACCACATGGTGGCTCACAACCACCCGTAATGAGATCTGATGCCCTCTTCTGGTGTGTCTAAAGACAGCTACAGTGTACTTAAGATATAATAATAAATAAATCTTAAAAAAAAAAAAAGGTCCATGCAGAGATAACTAACCAAACTGTGGTGTTCTTTTTTTCTTCCAAG
Seq C2 exon
GACATAGATGCAGTCCTTGCCCAGAAAAATGGAAGTGGTATGGAGACAAATGTTACCAGTTCTATAAAGAAAGTAAGAACTGGCAGAGTTGTGAATACTTCTGCCTGGCTGACAATGCCACCATGCTGAAGATAAGCACACAGGAAGAGCTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000033082-Clec1a:NM_175526:3
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact





	

	
ORF disruption upon sequence inclusion





No structure available

		

			
Features


			

				
Disorder rate (Iupred):
  C1=0.038 A=NA C2=0.000
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
PF043759=HemX=FE(41.8=100),PF041569=IncA=PD(68.7=95.0),PF061036=DUF948=PD(78.5=85.0)

							
A:
NA

							
C2:
PF043759=HemX=PD(21.7=58.8),PF0005916=Lectin_C=PU(25.5=52.9)

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000047065





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000129742, ENSMUSP00000132252
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chr12:10075656-10081236 
ALTERNATIVE
HsaINT0036187
(CLEC1A)
Human
(hg19)
chr12:10228255-10233835 
ALTERNATIVE
HsaINT0036187
(CLEC1A)
Rat
(rn6)
chr4:163197103-163200605 
ALTERNATIVE
RnoINT0037147
(Clec1a)
Cow
(bosTau6)
chr5:100313496-100314682 
LOW PSI
BtaINT0039185
(CLEC1A)
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






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