Special

MmuINT0096254 @ mm9

Intron Retention

Gene
ENSMUSG00000036792 | Mbd5
Description
methyl-CpG binding domain protein 5 [Source:MGI Symbol;Acc:MGI:2138934]
Coordinates
chr2:49169170-49172589:+
Coord C1 exon
chr2:49169170-49169245
Coord A exon
chr2:49169246-49171907
Coord C2 exon
chr2:49171908-49172589
Length
2662 bp
Sequences
Splice sites
5' ss Seq
ACTGTAAGT
5' ss Score
8.59
3' ss Seq
TTCCCCAACCTTATTTCCAGGTT
3' ss Score
8.04
Exon sequences
Seq C1 exon
AAGTGGGAAACTAAATAACCATTTAGAAGCTGCTATTCACGAGGCCATGAGCGAACTGGACAAAATGTCTGGGACT
Seq A exon
GTAAGTCAATTTATTTTTTTCCATTATTCTAGTTTCTTTGAAAATAAATTGCATTAACACTTTTTTTTTGTTAAAAAAATCTCTTGAACATTGTAAAGCAACTCTCATAGCAATACTAAACTGCCAGGCAAGCAAAAGACTGGCGGCAGAAAAGAATTTAAGGGAAGGGAGCCTGTATTAGCTATGGATTTTTTTTTTCTGAGATAAGTAACTTTTGTTTTCTTAAAAAGGTTCATTAAGTGGCAGCAGCAGTATGGTGAGGTCCCAACCCCAACTTTCTGAGTTTGACTGTGAGTTGCAGTGACCATCACTATAGCCAAAATATTCAGCAATGCAACCTCACTCCATACATTAAAAAAAAAAAAAGTAGGATTAAAAAGATTGGTCAATTTAGAGAGTATATTAACTTCTTATTTTCCTTCTGCTACCTTAAAATTGAGATGATTTGTGCATATTTCTGTTACTAGTAACTGTAAATCTCATGATTAAGGAAGAGATGTGCTTTCTCTTCACACTTTGTTTGACCTATGCATCCATTAGTTTGAGATGAGAGGTATAAAGCTCTCTCTCCATCACATACAGACTCAAACACATAAATATAATGTTAGTAATCTCTTTAAAATAAGCATTATTTCAGGCTGCATAGCAATGACAAGCCATTTACTTAGGCCATCTGAAACTTACAACCCATCCATTGGCTGCTTCATGATGGGTAACAGTTAGGGAGCCTCAAGATGTTGCCATTGGCACAGGTCATAGACATGTGTTAATCTAACCTATGATTGGATTTTGCCAGGAAACCTAAGTTTCCTGGTAAACTTGTAGCCATCAACTACAGTATCCTCTAGAACCAGGCATGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTAGTCTGTCAGTAAAGAGGATCAGGAATGAGAGCAACAATTCTAGAATTGAGAGTTGCCAACAAAAATGTGCCTGCTGCTGAGCCTGTTGAAACATAGGCCATGGCTCACTTGATTCTGGTGCCTGCAGAGGAAGGTGTAACTCTACTTGGCCACTTCCAGACCTAGATCCCTTCTTTGTGGAGTGCCCACCGCTCCTTGAGACCTTGATGTGCTCACCCCATCTTTGTATATCCTTTGCGTCCTGCTTGATAGTAACGAGAGAAGGCATGAAGAAATGTCAGTGTAGCTCCTATGAGCTCAGACGTCCTCAACTCAAGTGGGTGTGGAAATGCAGTTAATGATTTACCTTCCCAAGAAAAATATGAAAATGGGTTGGCCTTCATTTCATGCCTCTCTACCTTGGGGCATTTGGCCTTTGTGCCACCAGGCATTGGTACCTAATGAGGCCATCTTGGAATGTATTCTTCAGACGTGCTTTCTCCTTTGCACTGAGCAGAGTTGAGCCATGTGGGAAGGGGCACTGGAGTTGCCTCAACTCTCTTGAGAACCAAAATCTAGAATTTCTCATGTTTACAGTGGTTTCAAAGGTATTAAAGCACTTACACACAAACCTGTTTACAGCTAGTAAAACAGGTTTTCAGGCCATAGTTGATCCACAAACCACTAATTTGCTGTTGTGGATAAAGACTCTTTCCTCAATTACATAACTCCTCATTTCTGAATTTGTGCTTGTTTTAAAAACATGTGTGGAAAAGGGTCGGAGAAAGAGGCAGTCTGAGAAGTTCAGAGCATTATCTTAAAGTTTTAAATACTATTTGTAAAAAGAATTTTACCTTTGACTAAAAGCAAACAACGTTTGGTGTTGTCTAAACTTTATTTTAATTGGCACATTGTTGGTAATTGAATCTAGGGCTTCATGCATATTTGTAAAGCACTTACAGTTAACTCAGCCTCCAACCCTTAAACATTATATTCTAAACACATAGTTAAACCAACTGATTGTTTTCCTAGTCCTGTGACATCATGTTAGTAGGCTAAAATCATCTGTGATAGAAGTATTTAGACCATGGGAATTGGTAAATATTACAGTGCATTTGTTTCCAAATACTAGCTGTTTAACACACAGCTACTCTACTCTGCCTTCTGGGTCTTACTTTATTCTCTGACATCAGTAGCCATGTTACAACTTGGAAGATCTGATTGTTTGCCTTCTGCTCCTCAAAATGTATCTAGTACCATCCAACCCTTTCTCAATGTGACACACGGGATTAAATGCTTCTAGTTCCTTTATTAGTATATACCATTGCGTTCTATTAATTACTCTCCCCAGTTTACACAAACTCAGACCTGCCGGTGAATGACAGTGATGTTCTAACATCCATGCTGATTCTTCTCATGAACAGACATCCTTGGACTGAGCTACATGTAGCTGCTCTGATCTTTGACACTTTGTAGCAGTTATGAAACAAGGGGTGTTAGGAGAAGAACAAACGAATACTTGGTTTTAGCTGATTGAGGGAGCTCTGCTGGCTCAGACATGCTCCCCTGGTGAGTGGAGTCTTCTGGGTGTGTCTTTTACTGCTTCCCATCCCTTTTTGAGGCAGTGTTCCCACAGACTCAGGTCTTCATGATATTTTATAAAGTGTCTCAGGATATAGTGATTGAAAGTGAATCAGACTGTTTTCTGCCCTATTTCTTTGTCAGAAGTCATATGGTGTTTGTGATTCCAATCTTGCTGTTGTTTTTTCCCCAACCTTATTTCCAG
Seq C2 exon
GTTCACCAAATCCCACAGGGTGACAGACAAATGAGGCCCCCCAAACCCAAGAGGAGGAAGATCTCCAGATAACAGAGACTGTTCCACTGACACACAGTGTTGATCAAAGGAGCATGTACAGACACACCTGTATGTGGGTATTGATATGACCACCGTTAGATCAATCTGTAATCTACGGCAGATAGCTACCACCACCACAGGGCCCTAAAGGGAACAGCAATGGAGACAAGCATTGATCAGGAAGGAAAATGAATGTCAAAAGCAAAACAACAATCAAAATCCCTGTATGAACAAAGCGGTAAATGGTCACGTGATCGCTGAGAACGTTTTCTATTGTACTAAAATTGTGATTATAAGAAATAGTCCAAATGTTTCTGGAGAATTTTCAGTGTTGTATATAGAAAATACAGAATTTCATGGCGATATTAGAAATGTAAATATTGTACAATATTGTCATGTACAAGCATACTTAATGCACACTTTATCTTTTATTGTACAAAGAAATAGTGTACAAAAATCTTTGGTTTCTATGGAGTACACCTACCAGAGACTACCAGTGTAAAGTGATAAATAAAAATACAACCTAAATGCTTTTCTATGATAATGTAAAAGATGCTGGTTTTGTATTTAATGGCAGAGGAAAGGCATGGTGATGTAATACACACATCATGGCATACACTGC
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000036792-Mbd5:NM_029924:16
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact





	

	
Alternative protein isoforms





No structure available

		

			
Features


			

				
Disorder rate (Iupred):
  C1=1.000 A=NA C2=1.000
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
PF0085512=PWWP=PD(22.0=69.2)

							
A:
NA

							
C2:
NO

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000036847





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000108363, ENSMUSP00000108374, ENSMUSP00000119317
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chr2:148510136-148512869 
ALTERNATIVE
HsaINT0100393
(MBD5)
Human
(hg19)
chr2:149267705-149270438 
ALTERNATIVE
HsaINT0100393
(MBD5)
Rat
(rn6)
chr3:33501001-33503557 
LOW PSI
RnoINT0090113
(Mbd5)
Cow
(bosTau6)
chr2:47800962-47804933 
LOW PSI
BtaINT0090373
(MBD5)
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
chr7:36324949-36327423 
ALTERNATIVE
GgaINT0050080
(MBD5)
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"