Special

MmuINT0179437 @ mm9

Intron Retention

Gene
ENSMUSG00000078796 | Zfp541
Description
zinc finger protein 541 [Source:MGI Symbol;Acc:MGI:3647699]
Coordinates
chr7:16661696-16665175:+
Coord C1 exon
chr7:16661696-16661936
Coord A exon
chr7:16661937-16663320
Coord C2 exon
chr7:16663321-16665175
Length
1384 bp
Sequences
Splice sites
5' ss Seq
CCTGTATGT
5' ss Score
4.27
3' ss Seq
CTTTCCATGTTTCACTACAGGAC
3' ss Score
9.99
Exon sequences
Seq C1 exon
ACCTGGGGCTGGGCGCACTCAAGGTGCCTAAAGAGGCTGATGAAGGAGGCAGGGCCACTGGGAGTACAAGGAAAGGCAAGCGACAGCACAGTTCCCCTCAGAATCCACTCCTGGACTGCAGCCTGTGTGGGAAAGTGTTCAGCAGCGCCAGTTCCCTGAGCAAGCATTACCTGACGCACAGCCAGGAGAGAAAACACGTGTGCAAAGTCTGCAGCAAAGCCTTCAAGCGGCAGGACCACCT
Seq A exon
GTATGTCAAGAATCTGGCCAGAAGGGCAGGGGGCATGCACCTGTCCTCCTACCCTCTCCCCCATCCATCTGGTCCTCTGTTGAGTTCCCACTTCTGTGCTTCTCAGATGTATGTCCCCTGTCCTCCAGTGTGGACTCTGTTCTCTTCACACTGCTATTGTCTGGGGGCAGTCTCTTTACTAAGCCCCAAATTTACACCAGTGAGGAAATCCCTGTCTATTTGCAGACATGGCTCTTGTGGTTTCTAAATGTGATGAGTTACCAGGCGTGCTGGCACACTGGGGAGGTAGAAGCAGGAGGATCAAGAGTCTAAGGCCAGCCTCAACTACATACATTACAAGTTTAAAGCCCACCTGGATTATATGAGAAAGCAAAACAAAACAGTACAAATGAAGTTGGCTAACTTAGTAAAGAGATGCCCTAAGTCCCTAGCAGCTGTCTAAGGACAACAGGTCTGCAACCTGGTCATGCCCCCCCCCCCACCAAAAGCTGTATAAAAGCTTTGAGCAAAGTTCCCTTGTTATTAATGTCTCTGTTGCTGTGAGGCTCAAAGAGTGGAAGAGGACAATGCCTAGCTAGAGGGAGAGGTTTTGATAACCTCTCTTCACCCTCTGGCCTAGACTCACCTTAGGCAAAAGTCATTTTCTTCTAGGACTAATCCTTAGGTCTTTTGAGTCCTTCCCTCACAAGATCATGGACATTCTCTATAGAAAGACAGTAGTCATTAAAACATCCCAGCCATGTGCACTGGGATTGTCCAAAGCTAGATTGTTAGAACCCCAAGGGTGAGGGCTCATTGTTCACTCTGTTATTGTCCACATAAACAGGAGTAGGTACAACATATATGTACATGCATTTACACTTCCACACACTGCCTTTTGGCTCTAGTTTTATTAACTCTCTGTAAGTTAGTTTCTTGGCTGAAGGGGGAGCTGTTCCAGGAAGCTGTCCCCATACACAGTACTGTGGTAGTCCAAGATTGGCATCTCCTCAAATGTATTCTACAGAGCTCTACTTCTCAGGAATGCTGGTGGAGCTATATGAAAGCAAAGGTTAAAGATGATTCCCCACACACACACCAAACGCTTTGTGAACCTCCAAAGTGATGTGTGTGCATGTGTATGCATGCATGCATGCTTTTAACACACCCCTGTTGTGCCCAGGTCCCCAGAGCTTACCTCTAGAGAACTGTTGTTGTCTCTTGTGAACCCACTCTGGGGAAACCCGATCTGGCTTGCATGGGATTTCAGTGTTTGTTAGCGATGAGGGCAGAGAAGTGAGCCACCCCCCCACCCCCGTTGGTTAGACAAAGTAGGGGGCCCAAGCACTTCCTGTGTTGAGGTGTGAGGCTCTCCTGATGACCTCCTTTCCATGTTTCACTACAG
Seq C2 exon
GACTGGGCACATGCTCACCCACCAGAAGACCAAGCCCTTTGTGTGCATTGAGCAAGGTTGCAGCAAGAGCTACTGTGACTACCGCTCGCTGCGCCGCCACTATGAAGTCCAGCATGGAGTATGCATCCTGAAGGAGACTCCACCAGAAGAGGAGGCCTATGGGGACCCAACTCACAACCATGATGTGGCTAACCAGCCTCCACCCAGTGGCCTGAGGTCCCTGGGGCCCCCAGAAGCTAGGTCCCCTGGCTCTGTCTTGCCCAACAGAGACCTCCTTCGCTGTATTGTGAGCAGCATCGTCCACCAGAAGATTCCTTCTCCTGGCCCAGCAGTGGGGCCTTCTGATACTGAAGCAAGGAGCTCAGCCTGTGCTTGCCCCACCTCACTGGGATCATCATCATGTACACCAGCCAGCACCCCAGTGGCCCTAGGAACCCTGGGCTCTGAGATTCCTGAGGAAACTCATCCCCCACGGAAGGAAGCTGCCACCGAAGTGTTCACACCTGTCCAGTCAAGGGCAGCTGAGAATGGTGTCCCCGATCCACCAGAGTCAGAGTTGGAGTCAGAGTCTCCACGGCTTCAACGGCCATCCTCCCTGGAAGGCTGGCCAGAGGGCAGCTCTCTGCCTGCCTGCCTGCCTCTCTTCAGAGGCCACTCTGTCCCCTCAGGATCCCAGCCTTCCAGCCACAACTTCCAGTGGCTCCGGAACCTGCCTGGCTGTCCCAAGAACAAAGGCAGCAATGTGTTTATGGTCCACAAGCCCCCTGCAGTGGCATCCCGGGAGGGCTCTGAGGGAGGAGGCTCTGGACCCAGCAGCACCCCTACCTCAGTGGAGCCTTCACCCAGCCTGGGCACCACCCAGGAGGAACTCTTGCCATTTCCTCCTGCACTACTAAAGGCCCCTGGTGAGGCCTCCAGTGAAGTTCGGCAGGCAGCTGGGGAAGATGAAACCTGGGCTCCCAAAAAGTGCAAACCTGACTGTGAGTCATTCCCATGGCAGAGCCCCACTGAGCTTGGGCTCCAAGATGCACAGAACCCAGGTGGGCTCCCCTCAGATGCCACGCCCCTCTTCCGGCAGCTGTTCATGAAGTCACAGGAGTCTCTAGTAAGCCATGAGCAGATGCAGGTGCTCCAGATGATTGCCAAGTCCCAGCGGATCTTCTCCCATACTCAGGTGGCTACAGCCTCAGCCCAGAGACCAGGGCCCGAGGGCAAGCAGTCCACTCTGAAGCCATTGCAGGGGCCATGGCCACCACAAACTCTGCCACCAGCACCCACTGTAGACTCTTTCCAGATAGGCCCTGGACACTCAGAGCCAGAAGGATCCCCAGTCCGCAGGAGGAAAACTATGCCTGCGGTGTCCAGAGAAACATCTCCTGGTGGCCCTAGGCGAGACACAAAAGGAGGCCCCAAAGTGGCCTCTGCACCACCATCCCTCACAGGGCCAGGCCTGCTCCCCTCCCGGAATCCAGACAGCTCTTCATTGGCCAAAGGGACATTGGACCTGGGGGACATTATCCCCAATGCAGGCTCAAGGCAGTCCCAGTTAGGTGGAGATGAGCCAGCTGGAACCCAGCTGGTTGGGAAACAGGGGCAAGGAGAAAATGGCCTGGCTTCAGGGGCCATGAGAGGTGAGAAGGGTCCAGCCTGCCCCCGAGGTGGAGGCTACAGGCTCTTCTCAGGGCACCCCAGGGCCCAGAGATTCTCAGGTTTCCGGAAGGAGAAAGTGAAGATGGATGTGTGCTGTGCAGCTTCTCCCAGCCAGGTGGCCATGGCCTCCTTTTCATCGGCTGGGCCTCTGGCAGATCCACCCAGAGACATGAAGTCCAAGCTGACAATCTTCAACAGAATCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000078796-Zfp541:NM_001099277:2
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact





	

	
ORF disruption upon sequence inclusion





No structure available

		

			
Features


			

				
Disorder rate (Iupred):
  C1=0.383 A=NA C2=0.815
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
PF138941=zf-C2H2_4=WD(100=29.6),PF0009621=zf-C2H2=PU(65.2=18.5)

							
A:
NA

							
C2:
PF0009621=zf-C2H2=PD(30.4=1.1)

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000104149





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000131838
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chr19:47545981-47549244 
LOW PSI
HsaINT0187577
(ZNF541)
Human
(hg19)
chr19:48049238-48052501 
ALTERNATIVE
HsaINT0187577
(ZNF541)
Rat
(rn6)
chr1:77972460-77973842 
LOW PSI
RnoINT0168387
(Zfp541)
Cow
(bosTau6)
chr18:54947198-54949197 
ALTERNATIVE
BtaINT0165690
(ZNF541)
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: 
GCACAGCCAGGAGAGAAAACA

				
R: 
ACAGCGAAGGAGGTCTCTGTT

				
Band lengths: 
349-1733

			

		

	





	
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"