Special

MmuINT0005546 @ mm9

Intron Retention

Gene
ENSMUSG00000015488 | 5930434B04Rik
Description
RIKEN cDNA 5930434B04 gene [Source:MGI Symbol;Acc:MGI:1924317]
Coordinates
chr2:26865486-26869685:+
Coord C1 exon
chr2:26865486-26865625
Coord A exon
chr2:26865626-26869612
Coord C2 exon
chr2:26869613-26869685
Length
3987 bp
Sequences
Splice sites
5' ss Seq
TGTGTGAGT
5' ss Score
5.84
3' ss Seq
CATTGTCTCTTGTTTTGAAGCCT
3' ss Score
7.07
Exon sequences
Seq C1 exon
GGGGCTGCGCGCAGCGTTTAGCATGAGCGGCTCGGGCGCCGCCGGAGCGGCCGCGGGCCCAGCCCCGCCGGCACAGGAAGAGGGCATGACTTGGTGGTACCGCTGGCTGTGCCGCCTGGCGGGAGTGCTAGGAGCGGTGT
Seq A exon
GTGAGTATCGGGTCCAGGGAGCGGGCGTCCCCGGGGTTGCCATGGCTCCCGGCCTCAGGCCTGCAGTCCACCGCCGGAACTCGATGGCTTACTGCCCAGTTGTTGCGGCCCTGATCAGAGGAAATGAGACTCACAGAGGACGCGCGTCTGCCCCTTCCCGGCCCTGCCTCGGCCTGGTGATGCTTACCTGGGCTGGGGTGGGACTGCCAAGTTCCCAGCCTTTGGACAAAACTTGTTCATAAATGGGGGGCAGCTCTCCACAGGCTGGGAAGTTTGCTTGGGGGTCAGATGGTGCCAGGAGAAGAGTGGCCCCTCAGGGTGGCTGGGCAGTGATCGGAGTTCTCCTCGGGTTCCTACTGTCCACACTCTCCTAATGCTTCTCGTCGGCCTAGTATCCTCCACACCAGCAAGCTTTCTCTGCTCTTGTAAAGAGGAAGGCAGGTCCGCCTCTTCAGTGCAGCTATGTTGCTGGCCTTCCAAACAGTGTGTTTGCTAAATCCTGGGTGTCCCTTTCATTGTGAATTCCTAGAAGTCCAGGTGAGTGCTGGGAAGGCCCGAGGATCCATTGCCTACCTGGTACCAGAGCAGGAACTGTGTGGGTAGGGGAAGACTCATCCGTTTTCCTGTCTGGAGGAATACCTTGGAGCCCCATCTGTCCAGACGATCTTGCTAGTCAGATGGATAGGGTAGAGTTAGGTATGTGCTGCCCTGGTAAGGCAGCTCTGGAAGAAGTCTGCTGAGGTTGATCAAATCCTCTTCAGTGCAGTTAGCTAGTTCAAGGTGGTATTAAGGGGTGAGGGACAAGGAAGGGCCTGACCATGACCTGTAGGCGGCTATCCTCCCTCCGTCATGGTGATTCAGTCAGTGACCAGGTGATTTCTAGATTAGATTGACTTTGGAAATCCCACCCAGTCCCATACTTCCTGTGGGTACCTGTGCTACTCCCGAAGGCCTCCCTAATCCTCCTGCCGAGCCAAGCTATCAGTGAAACCTTACTGGAGACCTGTGGCCGTAGCTTAAATTGTTCCCTGAACCTGATCATTGGGATCAGGGGGGTGGACATCAAGGTTTTGAATACTGGCATATCATAGGAGGGAAGGATATCGTGTATTTGCTTTAAAAACTCAATAGGGGTTTGGCAGGAGCTATGGCTTAGCCGGTCACTTTGACATAGGGCTATCCTCTCTTGGAATGGAGGATATTCTAAGGGGCTTATTATTTATTGGAGGGATTTATTCTGGTCCCAAAGACCTCTGTAGACAGAGGAAGAAAGGATTATAGGGACATCTCCTTTATATGGAAGACATGAGCATTATTAGCACCCCAAGTGAGTGGATGTATTTGAGTCCTTGGTTGTCAAAGGACTCCTGTTCGTCTGAGTTGCGACCTGGTCCTCCCAAAGGTGGCTCTGTAGGACAGCATGGTGGAGTAGCTCTGTAGATGGAATGCTGAGGACAGGAGTGCAGGCCTTTCAGGTGAGACCAGGCCTAGCTCCACACAGGCAGGGGGCCGACAGTCTTTCACTTCTGTGGCCCTGGAAGCTTTGCTGCGTGAATGAGTGCTGCGTTGAGTTCTTTATTAGAGGAGACTTTGTGACATAGAAGCTGTGCCACTCATTTGGTCCATTCTCCTGCATCAGTTCCCATTTGGATAATGTAACACAGGAAAGTGGAAAATGGTGGAATTCCAGGCCCAGTGGAGGGATCCGGTGACCCAGGCCTGCTGCAAGTTTAATAAGTTGGTGCTAATTGCAGCCTCAGAGGGCCAACACTCTGCCCTCCCTTAGCTTGTGTCCTGCCAGAATGGGCAGCTCTCAGCAATGTCCTCAGAGGCTCCCAGAGTTCCTGGTGAGGGACTTCTTGGTGAAGCCTGGGTGGCTGGGGCAGACTGTAACCTGAAGGTGCAGTCAGAGGGGAGGGGCCTCGCTGGGCTTCCACACTGGAGAAGAGCACACACACTGTCCCCTCTTGGTGTCCTGCTATTCAGGTATTGGGGCACAACCTGCTCATGTGTAGGAGAGAAAAATGAATTAGGAAAGCAACATGTTCAGGGTCACGTGGCTAATGTTTTAGATGGGATTGTCATTTGAATCTTCCCTGGTGTATCATAAGAGGCATCCCTGTCCTGACCCAAATTCAAGATGTGGCCAGACGTAGTGAAACATGCTTGGAAGTCCCCAGGAGGCTGAGAGAGAGAGAGCAAGATAGTTTGAGGTCAGCTTGAGCTATAGAGCAGGACTCTGCCTCAAAGGAAAACCAAACCAAACACCCTCACCAAGCAAGCATAAAGAACAACCCCAAATAAGTCGGAGTGGCCTTTACCAAGTTAGAAGACATTTTTGAGTAGTTTACCTGGTGGCTGCAGACTGATAGGCTAAGATTCCCACTGAAGTCGGAACAGGCCTGACTTTTTAATTTTTTAATTTTTATTTTTTAAAGATTTATTTATTTTATATATGTGAGTACACTGTCTTCAGGCACGCCAGAAGAGGGCATCAGAACCCATCATAGTGGTTGTGAGCCACCATGTGGTTGCTGGGAATTGAACTTAGGACCTCTGGAAGAGCAGTCAGTGCTCTTAAACCTCTGAGCCATCTCTCCAGCCCCCCAGGCCCTACTACTACTTCCTCTTCCTCTTCCTCCTCTTCCTCCTCTTCCTCCTCCTCCTCCTTCTTCTTCTCTCCTTCTTCTTTGAAAAGATATCTCTCTTTATTCAGTTGAGATTGGATACATATTAGTGTATTCAGACTCATTAATGGGCATACAAGAGCTGAAAAACCTGGAAGCCATACTATATCATGGATTTTTTTTTTAAATGTTACAAAAGTCAAAGGATTGGCATATATTCTCAGAAAAAAAAAGGAGTTGACATACTTTTGTGAAAATCAGACTATATATAACGTGTTGTTTTTTGTTTTGTTTTAGTAGACGAAGCTTTAGTAGACTTCTCATTTTATAAGTAACACTAGTCAGCACAGCCCAGCCCAGCAGCAACCAGTGAGAGCCAGGCTTGAGGGCTCAGAACAGTCTACCTACACCAGAGTAGACCAGTTAGAACTCTAGTCTCATCTGGTGGTCTCAATATGAGAGGAAAAAAGACAAAAAACAAAAGAACAAAAAACTATGGAGCTAACAGAAGAAAATCAAAGTTTCTTAAACTAGGTTAGAAATCCGAAAGTATCAAGCCTGAGATTCTCCACCAAAGCCCATCCCACTCTGGAAGCTCTTTTCTATTTTCCCTTAAAAACAAAACAAAATTTCCTAACAAAAGCCAGCTGTCTACATTAAAATTAAGAATGTCTGTTTGGTGAAAACCCCCTAGATACACAAAGTGCTATTTTGAGGGGTTTTGCAGTGGCCAGAACACAAGCAACTCCTCAAGGAAAAGAGACGCACGCAAGAGGAAGCCACCTCCCGAGAAAACAGCCGCTGACAAAGAAAAACCAGAAGGTGGCCGTGCATAAGAAATGGTCTTCAGATAAAGGGATATTAAGATATGTGGTGCTTTATATACATTGACTACCAAAATCAGGATTTACAGCGACAGATGCTGGTAAAGATAAGGAAAGAGAAGCCCCAAGAAAGGCCAGTTTGCGTTCTAAAGAAAACTATGGAGAAACCAGGAAAATGAGCCTGTATAACCCACAGTCCCAGCCTGGACAGGTACACCAAAGAATGACCCACCCCGGCCCAGAGGGGACACATTAAAGATGTTCGCTGTCAGGCCTGACTTCTTGAGAGGGTTTGATAATAACCTGGAACCAAGGGGCAGCTCATCAGAGCCTTAAGCCTTTATATCCTCCAGGTATGAAAGTAGCTAGACTTGAGCTCAAACGTAAACTTACTACTCTCTGCTGTCTCAGGTGATGGTGGTTGCTGAGGGAAGCCCTAGTGCTGAGCGTCTAAAGGGAGCCTCATGTGTTCTCAGTGCCTTCTGCACACTCTGCCATACTCTGCTAACCCCTGCCCATTGTCTCTTGTTTTGAAG
Seq C2 exon
CCTGTGCCATCTCTGGACTCTTCAACTGCGTCACTATCCACCCTCTGAACATCGCAGCTGGCGTGTGGATGAT
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000015488-5930434B04Rik:NM_029862:1
Average complexity
IR-S
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:
PF085075=COPI_assoc=PU(26.5=45.0),PF102334=Cg6151-P=PU(9.0=17.5)

							
A:
NA

							
C2:
PF085075=COPI_assoc=FE(35.3=100),PF102334=Cg6151-P=FE(30.8=100)

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000109639





     
      









    
Other Inclusion Isoforms:
ENSMUSP00000122562
          









    
Other Skipping Isoforms:
ENSMUSP00000109636, ENSMUSP00000109637, ENSMUSP00000109638, ENSMUSP00000109639f5846A, ENSMUSP00000109640
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chr9:133460188-133463482 
ALTERNATIVE
HsaINT0025519
(CACFD1)
Human
(hg19)
chr9:136325310-136328604 
ALTERNATIVE
HsaINT0025519
(C9orf7)
Rat
(rn6)
chr3:5558822-5561759 
LOW PSI
RnoINT0027625
(Cacfd1)
Cow
(bosTau6)
chr11:104408380-104411527 
LOW PSI
BtaINT0092590
(MGC139698)
Chicken
(galGal4)
chr17:6927238-6930894 
ALTERNATIVE
GgaINT0126400
(C17H9ORF7)
Chicken
(galGal3)
chr17:7595287-7600644 
ALTERNATIVE
GgaINT0126400
([1])
Zebrafish
(danRer10)
chr21:5845934-5852109 
LOW PSI
DreINT0005627
(CACFD1)
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"