Special

MmuINT0133094 @ mm9

Intron Retention

Gene
ENSMUSG00000075376 | Rc3h2
Description
ring finger and CCCH-type zinc finger domains 2 [Source:MGI Symbol;Acc:MGI:2442789]
Coordinates
chr2:37256049-37260939:-
Coord C1 exon
chr2:37260764-37260939
Coord A exon
chr2:37256250-37260763
Coord C2 exon
chr2:37256049-37256249
Length
4514 bp
Sequences
Splice sites
5' ss Seq
AAGGTAAGC
5' ss Score
10.22
3' ss Seq
TTTTTCCTTCCCATTTTTAGGTT
3' ss Score
13.35
Exon sequences
Seq C1 exon
CTATGCAAGAAGAAGCCTTGAAGTTGGTATTGCTGGCATTAGAAGATGGTTCTGCTCTCTCTAGGAAAGTTCTAGTACTTTTTGTTGTGCAAAGACTAGAACCAAGATTTCCTCAGGCATCAAAAACAAGTATTGGCCATGTTGTGCAGCTATTGTACCGAGCTTCTTGTTTTAAG
Seq A exon
GTAAGCCCTGTACAACTGTCCAAAGACCATGGGTTTATACCTGAGATGGAGGCTTCTGAGAATTTATGTTGCCAATCTAGTGACCCTCAGAAATACAGAACACTTCTAAAGTAAAGAGGAGTGGTTTTTCACTTTTCCTTATTCATTAATTCATCTTTGACACCAGATACTTGTTATTACCAGTTGGTTTCAGAAATATTGAATTGAACATATGTAAAATCCTAACTTTAGACTCTTCGAGGAACTTGTAAAAATGAATTGAGACATCTCACTTCTTTACATCAATTGCTTTAACAAATATTGCAGACTTCGATAGAGGAGGAAATTTTTTTAATTCATTATTTTCTTTATCTTTTTTGTACTGATTAAAGTCTTCAATATAAAATTAGTCCACAAGAAATTCAAAAGTTGAGAAGATTGCCATGCTGTATGGTATTTTGTTTGATGGGATGTGAAAACTATTTTTTAATGGAATTTTTAGGTCATTGATAGATGAGAAAAGTTACCTGAATCCCTGTTTTCTATCTGTTAACAGTTGTGGAAAATATTTCATCTGTATCAGGGGCTTCTACCCTGCCTTTGATTATTCAGTTCCCTGATAAAAGACAAACAACTTTTTTTAATTGTAATAACCTTTAAAGGGGCTAGAGAAATGGCTCAGCAGTTAAGAGCACTGACAGTTCCTCCTGAGGTCTTGAGTTCAATTCCAAGCAACCACATGGTGGCTCACAACCATCTGTATTGGGATCCAATGCCCTCTTCTGATATGTCTGAAGACAGCTACACTGTACTTACATACATTGAAAAGAAAGAAAAGAATAAGCACTAGAACTGGGTGGATATCTACTCTCTAAGCTAATAAAATCTATTTTCCCATCAATAACCCTGAAATATAATTTGCCATGTTCCATCTAGGCTGCTTTGACTCACATTACCCATAGCATGAAAACACCTTTCTATCTCTTCTTGTGGTTCTCCTCATACCCCAAACCTGCCTATGTCTCTTCTGCATAGCTATTAACCATAGTTTTAGATTAAGAAGCAAGGTCACATTGTATGTGTCAATTCTCTGGTCCCTGGGAGCAATCAGGCCTTGGGGGCCAGTATTTAGCTTAACATACATAGCAAAAGAGCAAACCTCAATAGTTATTCAAGTGTAGGTTGTTATCTAGCACCTGAAAAACCACAGAAATTTATAAATCTCACTGTTTTTGTGAAAGTAAATCACACGTTACCTTCCTTTGCTCGTTTTCAGGCTCTAAGATTTAAAAAGGTTTCCTTGGAAGTACTCTAATTTAGAAAACAGGTAGTTGATGATGGAAGTATGTTCAAGTGGATTTATTTACCTTTGCTAATGAAGTTTGGATACTTTTGCCTGATAGTTGTAGTGCTTGAGTTCATGTCCTTAAAGGAGATAAGGATTTAAGTGATGCTCTGGTTCTTCAAACATAATGTTTTCAAGCTGAGTAGCCAAATTAAAGAGATCATTTGTCATTCTCATTTGTCATAAGCAACCAGATTTTTGTGATTGTATGATCTTTCCTCAGAATTAAGATCGCTATAATCATGATCAAATACAACAGATTATCAGTTAAAGTGATTTCTAATAAGAATTGTAATTCATGGCAATGAAATAACTTTGTGGATAAAGGTGCTTTGTCTTCTGAGCCTGAGGACAAGTTTGATGCCTGAATCCCACATGATAGAAGGAGAGTGCTGATGGCTGCTACTTTTCCTCTCATGTCCACACACGTGCAGGCATGTACATGCCCACATATATACTTACCAAATAAATAATATCCCTATATTGATAGATACTTTTATATGCAGATTCTTTGCTTACTGGACATGGAATCAGAACAAGGAGAATTAAGATACATGCATGGTGTGGTGGTTCCCAACTGAAAGCACAGCATTCGAATCATCTGCATTATGTTTCTGGGCTCTAATACCAGGAATTCTTATTCAGTAGATTTGAGAGTGTGTCTTTCAAAGCTTCATAAATAAGATGTGATTGCTTTGTGTTGGTTTTAAAGACATGTTCTCCTGTATCCTAGACTGACCTTGACCTTGTTATTTGGTGAGGATGACTTTAAACTTTTGATCCTCTTCTTTTTTACCTCTCAACTGCTGGGATAATGGGTGTGCATCACTGCAATGTTTATTTTTTAATGTAGTGCTGGGGATCAAACGTCCCCTTTGTTCATGCTAGGGAAGCATTCCACCAACTTAGCTACAACTTTAGCCCTTCACAAATGATTTTGGTGCATATTAGTATTTTAAATGGCTCGGACTCTCTTTATTACTGAAGTCTTCAACTGCTTAGGTGCTTTTTGCTATCCATGGGGCACATGTACACTATATGGTGCTTAGGTTTGTGCTATAATCCTCTAGATAGTTAGTTTTCTCCTCCCATTTAGGTTAATAATTACCCCCTTTACTTTCTGATATTCTCTTAAAGTGGGTTATAGAAGAATACAAACTTTCTAAGTTACATTTACCTGCCCACTCACTATCAAATGTTTAAGATTGTATTGATTGGGGCTGGAGTGACGAATGGCTCAGTGGTTAAGAATACTTGCTGCTCTTAAAGAAGACCTGGGTTTGATTTTCAGTATCTGTATGGTGGTTCTGGGGAATCTTGATACCCTTTTCTGGCCTCCATGGACACAAAGTAACACCTGTGATGTACAAATATACATGCAGGTGAATACTCATTCACATAAAATAAAAGAGCATATTAATTACAATCTATAATATCTCAAACTATATTTTTAGATTCCCAAATTTATGGCCTTTCTGAAGTGATGACTGACTTTTCTCAGTCTCATGTTATTGGGGCATATTACCACTGTCTGATATACCAGCAGCAGAAATAAAAATCATTACTAAAGCAGGACATAGAAGTCTACACCCCATAATCCCAGTACCTGGGAGGTTCAGCCAAGGGAATTTCTGCAGTTTTGAGGCTATGTTAGGTGACAGAGTAAGACCCTCAATACACACATAACCACTAAGATAGCTGGAGGGTTTTTTTTTTTTTCATTTTTTTTCTTTTACCAATTAGGAAAACAAAATTATGTTGTTATGACAGGGTCTTATTATATAATACAAGCCAAACTTTGTGCTCATGATTCTTCTGTTTCGGCCTCTTGAATGCTCGTATTTTAGGCATGCAGCATCATGCTCAGCAGGAAAATTTGAGTTTTGAATAGATAAATGATTTGTCCAGTCTGAATCTCAAATTTTGGTGTGGTTTTATGTGCTTTGAGTCTTAAGTCTCGGAGCTCATACAGTGAGATGGATGAAAGACAAAAGAAAGTTCCCAGAAGCTATGGCCAATACAAACAAAATCGAAGATGAAGATTCATTCCCAAGGTTATCCTCTGACCTACACACAGACATATACAGACACACACAGACTTAATCGCAGTTAAAACAAGGAAAACACTTACTTCGCGTAGCACTGTTCTAGGTACACAGTTTCAATCTTAGGAATTCTAATCTCCTTTCTGAAACTACAATATCTATCTGGATTTCTCAAAGAACCACAGTAAATAATGCTCCTACTAATCTACCCCAGCCCTCTTAGAAAAGTTGTGATGTACTCAGCCTGTTCCTCCTCAAACAAGAAAGCAGTAGTCTTTTTCACTAAAACAGTTAAACAAAACAAAACAAGACAAGAAACCCCCACTTTCTAAGCAAGGAAAATGATAGTGTTTTTGAGACATGTGTCTAATCATAGTGCTTCTGTAACAACTCTCAGTGACTTTTCATTCCCTTCAGAATTTAATATCTAATTTACCATAGTACTTACGGTCATCTGTGAGTCTTTTCTTGCATATATGAGAACTTTTAATTCTGTCCTCTGCTCATTTGGGGTGGTTGGTTGGTTTGTTTGTTTAGTAGGTTGCTGTTTTGTTTTATTTTCTCCCATCTTCTAGACAGGGTTTCTCTATGTAGCTCTGGCTGTTCTAGAAATCACTGTGTAGACCAGGCTGTCCTTGAACTTATAGAGAATTGTCTGCCTCTGCCTCCTGAGTGGAGTGCTGGGATCAAAGGCATATTTTACCACTGCCTGGCATTGTTTTTTAGAATTTGATTTTCCTCTTTTTCCTAAAGAAATTCTATTTTTAGAGATGTAGCTCACATAGTCGTGAGCCAAGAGAAAACATTTTCTGAAAATTTTCCTTCTATTTACTTGTCGTATTTATTTGGCTTTGTTTATGTTGCTGTAGACCCTATAACTACACCCTTACTATAATTTTTTGTTTCTAAATCTTTCTTTCCTGCCAAATGCTGATGAACTCAATGAAGAAAAGGATTGCGTACATAATTATATACTTTCTGTTTTGTTCTGAAAAGGAGTTTCTATTGGCATTTTGTACTTTTTGTGGTGTCTGGTATATAACCCCTTCAGCCCAATCCCCACACCCACAGTAAATGAACTGGATAAGAGAAAAAGGCAGACCAATTCTAATGAGTTTGATTTTTTTTTTCCTTCCCATTTTTAG
Seq C2 exon
GTTACTAAAAGGGATGAAGACTCTTCCCTGATGCAGCTAAAGGAGGAATTTCGGAGTTACGAGGCACTACGCAGAGAACATGATGCCCAGATTGTTCATATTGCCATGGAAGCAGGACTCCGTATTTCACCTGAGCAGTGGTCTTCACTGCTGTATGGGGACTTGGCTCATAAATCACACATGCAGTCTATCATTGATAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000075376-Rc3h2:NM_001100591:6
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=0.015
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
NO

							
A:
NA

							
C2:
PF0028516=Citrate_synt=PU(25.5=58.2)

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000097721





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000108556, ENSMUSP00000108558
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chr9:122880795-122883203 
ALTERNATIVE
HsaINT0138840
(RC3H2)
Human
(hg19)
chr9:125643074-125645482 
LOW PSI
HsaINT0138840
(RC3H2)
Rat
(rn6)
chr3:21653760-21658475 
LOW PSI
RnoINT0125468
(Rc3h2)
Cow
(bosTau6)
chr11:94037688-94043391 
LOW PSI
BtaINT0123572
(RC3H2)
Chicken
(galGal4)
chr17:8795344-8795779 
ALTERNATIVE
GgaINT0125466
(RC3H2)
Chicken
(galGal3)
chr17:9504390-9504825 
LOW PSI
GgaINT0125466
(RC3H2)
Zebrafish
(danRer10)
chr10:9776872-9778917 
LOW PSI
DreINT0125626
(rc3h2)
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"