Special

MmuINT0132987 @ mm9

Intron Retention

Gene
ENSMUSG00000037070 | Rbmxrt
Description
RNA binding motif protein, X linked-like-1 [Source:MGI Symbol;Acc:MGI:1343045]
Coordinates
chr8:81029168-81032827:-
Coord C1 exon
chr8:81032698-81032827
Coord A exon
chr8:81030763-81032697
Coord C2 exon
chr8:81029168-81030762
Length
1935 bp
Sequences
Splice sites
5' ss Seq
TGGGTAGGT
5' ss Score
6.86
3' ss Seq
TAATACAATAATATTCACAGGTG
3' ss Score
3.53
Exon sequences
Seq C1 exon
GTTGACGTTGCGCGGGGGGAGGGGAAGCCATTCGCGGCCTCTGGTTCTCGGCGGGAGCGGCGGCGGCAGACGCGTGTGGCGACCGGCGCGGGAAAGCGGCTTCCTAGTTAGGGAAGCGTTAGCCCCGTGG
Seq A exon
GTAGGTTGAAAATCGGTGGCCGAGCAGACGTCCGGGACGGCAGGCCCCCCGCCTTCCCGCAGCGGCGGCGGCGGGAAGGCGGGGAAGGCGGGCTGGGCCTTCCCGCCAGGTCGGTGGCCTGCCCGGGCCTTTCTGCCCGACCGCCTCCGCGGCCAAAACCCGCCTCGGGAGTGGGGAGGACGGCCGGGATGGGGCAAATCTTCCCTGGGGGGCGGTGAGAGAGCGACCCAGGCTCCTCCCCACCCGTGTGCCGCGCGTGGGCGGGCGATTCCGGAGGCCGCGTGGTGCGGGCCTTTGCCTGACCCCGAACCACTAAAGCAACAGGACAACTGAGAGGGGGCCAGGAACTCAGAACAAAAGCAGTGAGGGCCAGATCCAGGGTGGAGGGTCTGATGTCCGCCCCCTCCCCCAACCCTCGGTTTCTTGCATTGCATTTTGGCGAATCTATGACATAGTTTCACGAATGGTCTTCCGAGCATCAACCCTTCCTCTTTATGCACCCAAAGAAAGAAAGGAACAAAGTATTGTGGGACATTTTGAAGCAGCCTGGTATCAGCTACTTGAATAGTTTACTATGGAACGTAACGTTCGAAAGGGATTGTACCAGACTTTCATTCTGAATGCATTCAAAGCTTGAAAGAGACTCGGCGTGCAATTTGCTCTATTTAACTTTATCTTGCTGACATGACTCGCTATCCAAAAACTAAGCTGCTTTAAGCAGTTGTGCTATCAGTTCTCAGTTGCACAGCCCCCACTGCTCGGTAATTACGCATCAGGCAGCATGAAGAAAAGCTAATCTCAAGATAAAAAGAACTTAATAGGGAGACATTAAACAATTTACCAGGCAAAAGAAGTACATGAAATGTGATAAAGGCTTATTATAAGACAGTCACAAGGTAAGTGGAGTTCTAGGAAGTAAAATTTATAACATAATTTTCTTCAGTAATTTTGCTTGGTTCAAAAGGAAAAAAAAATCTGCCTCAGTCATCGAATACTCAAAAGGTCATCACAGATAGTGCTGCTTAAGTAAGGCTGCTCACAGAGTCTTTCTAGAGATTTTGACCTGTTTAGAACAAAATCTTAATTCATAGAATATTTTAACCGTAGTTTTGTGAATTGTATTGTCAAGGACTGTATTAGTTTGCTAGGGCTGCTATAACAAATAGTCCCCTCCCCGAGTTAGCTATACTCAGACAATAGACATGTTGTTTTACTGTTGCAGAATAAGGAAATCCAAAATGGAGATATTGGAGGGCCATGTGTTCTAAAGGCTCTTTCCAGCTTCTTGTGGCTGTTAATATTCCCTGGCTTCCTTGATTTAGGTTCTGATGCTCCAGTCTCGACCTGGTTAGGCATCACATCTCCCTCCATATGTTTCAAGTGGCTGCTCTCTGCATCCTTGAGCATTCATTACCTTTTTTCTGTGTGTATCTTTAAAAGATACTTGTCCTTGGATTTAAAGCCTAACCAGATAGTCCAGAATAATGGGTCATATTCATTTAGATTAAGTTTATGAGCCTATATCCTTTCTCCAACTTAACTGGAGTACCATCCCCTGTAAAAGACACGTTTTCCCATGACCTCAGAAGGTGACTTGTAGAAATCAGATGTTGATAGGTATGAAAAGCTGCAGTTCTTCTGAATGTCATACAAAGGTGTGCAGGTGGAGTGTAAGCACCACGTAGGGTGGAGAGAGGAACTAGATTGAGATATCTATAAGCCAAAGTAGTCTAAGAATTACTGACAACCACTGGAAGCTAGGAGGGAGTCATGGTACAGATTTTTGTTAAGGCTTCTGATAGAAACTTACCTTCATACTTCGTGACTTCCTGAACTGTAAGAAAATCAATGTTTTATAACACACCTCCCACCCCCAGCCCTTTCGCAATGCATTGTTACAGCAGCCTGAGGAAACTAATACAATAATATTCACAG
Seq C2 exon
GTGCTCGTGTGCAGTAGTCCTAGTGGCTTTTCTGTTCTGTTCTGAGACCCAGCAGCTGTCACCGGTGAGCTACTTGGAAGGCCGATTTGGCGAGCTTGTAGGAGGAGCTTGAGACCTTCACGTCCCCTCCGACTCTCAGCTGGAAGGCAAGATGGTTGAAGCAGATCGCCCAGGAAAGCTCTTCATTGGTGGGCTTAATACAGAAACAAATGAGAAAGCCCTTGAAGCAGTATTTGGCAAGTATGGACGAATAGTGGAAATACTTTTGATGAAAGACCGGGAAACCAACAAATCAAGAGGATTTGCTTTTGTTACCTTCGAAAGCCCAGCAGATGCTAAAGATGCAGCTAGAGATATGAATGGAAAGTCCTTGGATGGAAAAGCCATCAAGGTGGAGCAAGCTACCAAACCATCTTTTGAAAGTGGCAGGCGTGGACCACCTCCACCTCCAAGAAGCAGGGGCCCTCCCAGAGGTCTTCGAGGAGGAAGTGGAGGAACTAGGGGACCCCCTTCACGTGGAGGATACATGGATGATGGTGGTTATTCCATGAACTTTAACATGAGTTCTTCCAGGGGACCACTTCCAGTAAAGAGAGGACCACCACCACGAAGCGGGGGTCCCCCTCCTAAAAGATCAACACCTTCCGGACCAGTTCGAAGCAGCAGTGGAATGGGCGGAAGAACACCAGTGTCCCGTGGAAGAGATAGCTACGGGGGTCCACCACGAAGGGAACCCCTGCCATCTCGCAGAGATGTTTATTTGTCCCCAAGAGATGATGGATATTCTACAAAAGATAGCTATTCAAGCAGAGATTACCCAAGCTCCCGAGACACCAGAGATTATGCACCGCCACCAAGAGATTATACTTACCGTGATTACAGTCATTCCAGTTCCCGTGATGACTATCCATCAAGAGGCTACGGTGATAGAGATGGATATGGTCGGGATCGTGACTATTCAGATCATCCAAGTGGAGGTTCCTACAGAGATTCATATGAGAGTTATGGAAACTCACGCAGTGCACCCCCTACACGAGGGCCACCACCATCTTATGGAGGAAGCAGTCGCTATGATGATTACAGCAGCTCACGTGATGGCTACGGTGGAAGTCGAGACAGTTACTCAAGCAGCAGAAGTGATCTCTACTCAAGTGGCCGTGATCGAGTTGGCAGACAAGAACGAGGGCTTCCCCCTTCTATGGAAAGGGGGTACCCTCCTCCACGTGATTCCTACAGCAGTTCAAGCCGAGGAGCGCCAAGAGGAGGTGGCCGTGGAGGGAGCCGATCTGATAGAGGGGGAGGCAGAAGCAGATATTAGAAACAAATAAGACTTTGGATCAAGGTCTCCATGCAAAGAAACAAAGGATGGAAAGTCTTCTGTCATAACTACCCAAGGACTACTAAAAGAAAAGTTGTGTTACCTTTTTAAATTTTCTGTTTTAAGTTTCCCTTCATTTTTGTGTTCTTGTGAAGAAAAAGTAAAACATGATTAATTTTGATATTATGAATTGCTTTCAACAAGCAAATGTTAAATGTGTAAGACTTGACTTGTACTAGTGTTGTAATTTTCCAAGTAAAAGTGTTCCTAAAGGCAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000037070-Rbmxrt:NM_009033:1
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact





	

	
5' UTR





No structure available

		

			
Features


			

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

				
Domain overlap (PFAM):

					





						

							
C1:
NA

							
A:
NA

							
C2:
PF0007617=RRM_1=WD(100=18.3),PF080816=RBM1CTR=WD(100=11.6)

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
NA





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000048153
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
No conservation detected
Human
(hg19)
chr4:147443683-147445340 
Rat
(rn6)
No conservation detected
Cow
(bosTau6)
chr17:11922272-11922823 
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
chr4:32678422-32678738 
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected




Primers PCR

	

		

			
Suggestions for RT-PCR validation

			

				
F: 
AGTTAGGGAAGCGTTAGCCCC

				
R: 
GCTGGGCTTTCGAAGGTAACA

				
Band lengths: 
355-2290

			

		

	





	
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"