Special

MmuINT0180017 @ mm9

Intron Retention

Gene
ENSMUSG00000074472 | Zfp872
Description
zinc finger protein 872 [Source:MGI Symbol;Acc:MGI:3588272]
Coordinates
chr9:22001819-22006567:+
Coord C1 exon
chr9:22001819-22001879
Coord A exon
chr9:22001880-22003861
Coord C2 exon
chr9:22003862-22006567
Length
1982 bp
Sequences
Splice sites
5' ss Seq
AAGGTGAGT
5' ss Score
10.47
3' ss Seq
TGTGATTCTCAATCTCACAGTGC
3' ss Score
7.96
Exon sequences
Seq C1 exon
GGGAAAATTGGCAAGACCAGAGCATTAGGGATCAGTGCAAAACTCAGGGAAAATACATAAG
Seq A exon
GTGAGTTGTACTCATTAAAGAACTGGAGTCCTATGATGGAGTCTTAGTATGTCATTGGAAACACAACAAAACTCCAATTTCATGTTTTTTTATCATATAAAATATAAATATTTATATTTTAAGTAAAATACATATTACATTTTGTTGTTGAAATCATATAATTTCAACCTAGAATTTCTACCCCGTCTTTGACCCTTTAGTTCCTAGACAAAAGACACACACAGCCTTTATGTTTACAATAAGCCTTAAACAGTCCCAGAGCCAGGCGGATCCCTACCCACTATGCTACTAGAACCTACTTTCCCATCAGTGACCCCAAGTTATTACTTATGACCTGCTGTGTTTCACCTAGGCTGCTCTGAGCCCCAGTTGCCCAGCTGTCAGGGCCATGTTTTTATGGCTCACCTAATCCATGCGGTTTCTCCTCCTTCCTCCTGCACCACCTTCTTAGACCCCAAGGCCAGGAAACCCAAACCCACCTATGTCTCTTCTGCCCAGCTGTTGGCAGTTGACATGTTTATTTACCAATCTGAAATAACTTGGTGGCAAAGTCTACATGCGGACTGTCTTGGCTCTGGGACAACCAGGTCCTGGGGGCTACATTCAGCATTACAATAAATAACAAAAGACCAAACCTCAACACCTATTTTCGAAAGGGTCCATGATTTTTTAAGATTTTGTTTTTGGTGCTGGAGAGTTGAGTGAGTGGTTAAAGGTACTTGCTGCTTTTGTGATGGACCTGGGTTCAGTTCTCAGTACTGAAATCAAGTGATTCAACCTCTGGTAACTCCAGCTCCCGGAGATATGATGCCCTCTACTGTTTTCCATGGGCACTGCACCCACATTGTACACATACATACAGGCAGGTGCATACACATAAGTAGCAAAAAAAGTAAATATTTATTTTAAATTACCTGTGTGTGCATGAGTTTGTGCATATTTACGTATCGTCTGAGGATTGCCAGAAGATGGATTACCTGGAGTCACACGGTATTGTGGGTTGCCCAGTGTGGGCGGGAACCAAACTCGGGTGCTCTGGAAGATCAGTAAGTAACCTTAACCACAGAACCATCTATCGCTCCAGCCTCCTAAGAGGATGATGTCATCCTCTTTTCCCTTTTTAAAAGTTTTTTTTTTTTATTCGTCTTAATTTATATGTCTCTGTGTGGGCATGTTTGGACAAGCACAGGTTCCCACAGAATCTATAGAGCATCAAATTCCCTGGAGAGCCAGAGTCAAAGCTGATTGGTTATATGTACCAGATGTGGATGCTGGGAGCCAAACTCAGGTCCTCCATAAGAGCAGCCAGGGCTTTTTTTTATTTAGGTTTTTTTTCTTCATTGTTGTTTTTTATTTTTCGAGACAGGGTTTCTCTCTGTAGCCCCGGCTGTCCTGGAACTCACTCTGTAGACCAGGCTGGCCTCGAACTCACTGAGATGCACCTGCCTCTGCCTCCGAGTGCTGGGATTAAAGGTGTGCACTACAATTATCCAGCTCACCAAGAAATTTTCAAACTGATACAGCCGAGCAGTATTCAAAGAATAACTCCCCTTGAAACAGTGTTAAGAAACTGCATGTAAAAACAGAAATAAACCACACAATATGAATATCACTTATAATTTTTTTAGATGCACTTATTTTATGTGTATGGATGTTTTGCTTCCATGTATGGGTATGTACATGCCTAGTACATGCGGAGTTTAGAAGGTGGTGGATCCTTTAGATCTGGAGTCACAGGCAGTTTTGAGCTATTACATGGGTGCCTGGAACAGAATCTCAGTTGTCCGCAAGAGCAGCAAGCACTCTGGACTGCTGAGTCACCTCTCCAGGCCCAGTGTCTTCATTTTCATAATATCTGTGCTCAAACTCTTTTAGAGTACTCATTTTGTACATGCTCCTTGAAAATAGAAAAAGTATAATCTATGTTTATGACATCATGAATGATTATAAAGTTGTTAATAATGTGATTCTCAATCTCACAG
Seq C2 exon
TGCTCATGTAGAACAGAGACCCCGCGAATGGAAAAGTGCATGCAGGGAAGTCTTCACCCAGCTTCCAGCTCTTAAACAGCAGCATATTCTCCCTGGAGTAAAGCCCTGTGAATGCGGTATATGTGGAAAAGTTTACTCCTGTCGTTCCTCTCTTAAGAGGCACATGCAGTGTCATAGTGAGCACACACAGTGGGAGAGTCACGGATTCAGAGGGAAGTTATACCAGTGTAAGGACTGTGGGAAAGCATTCAGCTTTCAAAGTTCATTTAGAATACATGAGAGGACTCACACTGGAGAGAAGCCCTACATGTGTAAGGAATGTGGCAAAGCCTTCATTTATCACACCACTTATCAAGGACACATGAGGATGCACACAGGAGAAAAACCCTATAAATGTAAGGAGTGTGGGAAGGCTTTCAGCCACCCCAGCTTGTTTCGAAACCACGAACGAGCTCACTCTGGAGAGAAACCCTATGAGTGTAAGCAGTGTGGGAAGACCTTCAGATATTACCAAACCTTTCAGTTACATGAGAGGACTCACACTGGAGAGAAGCCTTACCAGTGTAAGCAGTGTGGGAAAGCTCTCAGTCGCTCCACATCTTTTCGAAGTCACGAGAGGATCCACACTGGAGAAAAACCATATAAATGTAGAAAATGTGGCAAAGCCTTTAGATTCCCCAGTTCCTTTCGCAAACATGAAAGAATTCACACTGACGAGAGGCCTTATGATTGTAAGGAGTGTGGGAAAGCCTTCATTTCTCTCCCAAGCTTTCGAAGGCATGTGATATTGCACACTGGAAACGGGCCTTACAAATGTAAAGAGTGTGGGAAAGCCTTCGATTGTCCCAGCTCATTTCACATTCATGAGCGAACACACACTGGAGAGAAGCCCCACGAGTGTCAGCGGTGCGGGAAGGCCTTCAGCTGCGCCAGTTCTGTTCGAATTCATGAGAGGACTCACACGGGAGAGAAGCCCTATGAGTGTAAGCAGTGTGGGAAGGCCTTTAGTTCCTCTAGCTCCTTTCGCATGCATGAACGAATTCACACTGGAGAGAAACCCTATGAATGTAGGCAGTGTGGGAAGGCCTTTAGCTTCTCTAGCTCCTTTCGCATGCATGAGAGGACTCACAAGGGAGAGAAGCCCTATGAATGTAAGCAGTGTGGGAAGGCCTTTAGTTCCTCTAGCTCCTTTCACATGCATGGATGAATTCACACTGGAGAGAAACCGTATGAATGTAAGCAGTATGGGAAGGCTTTCAGCTGCTCCAGTTCTGTCCGAATTCATGAGAGGACTCACTCGGGAGAGAAACCCTATGAGTGTCAGCAGTGCCACAAGGCCTTCAGTTGCTCTCATTCTTTCCGGATCCATGAAAGGACTCACACTGGAGAGAAGCCCTATGAATGTCAGCAGTGTGGGAAGGCCTTCAGATGTTCTCGCTCCTTCAGAATACATGGAAGAACTCATAATGGGCAATGATCCTTTAAATGTAAGTCATGTGGTAAAGCCTTCCATTGTCCCACTGCCCTTTGAAGATACTCTCTTGCTTAGAGAAATACTGTGAACAAAATAGAACTGGAAAACCTCTCATTTCTCTAGTTGTGAATCCCAGAAAAAAAAAAACCCTATGTGTCTATGTGATGGGAAAACCTTCAGTGGATATGCAACTTCATAAGGCCACATAGATACACAGGGGAAAATAAACCCCATACATTAGGTAGTGTATAAAAGTCCTCAGTTGCTCAGTTATCTGGAAACCACAAACTTGTATTACAGGATAGCTTGATGAATGCAAGCATTGTGGGAAACCATCAGTACTCTGCGCCTTCCAAACATGTGAAGAGGACCCTTAAGAAGTGAAAAGTAATGATTAATTTCCTATCTTATTGAATATTTACATGATACTTATTTGAGAAATTGTGAATTTATGAAGATAACCACTGGAAAGGAATTCTGTAAGTGTGGACAATATGAGGAAGTTCCATGTAAGTTTGTATATGTATATTTTTGAAAAGTCATAAAATGAAAGAAAGGGAGTTTTCTTTTGTCATATGCTCATTCTTTTTTTTTTTTAAAGATTTATTTATTTAACTATGAGTACACTGTCACTGTCTTCAGACCCACCAGAAGAGGGCATCCAAATCCATTACAGATGGTTTAGAGCCACCATGTGGTTGCTGGGAATTGAACTCAGGACCTCTGGAAGAAGAGTCGGTGCTCTTAACCACTGAGCCGTCTCTCCAGCCCCCATATGCTCATTCTTAAAACTGTGACTCTGGACTATAGATTTTTGTTACTTTTGCTTATATGAGCATTGAGGTTAGATTATTCTGAAAGTCATCATTAAATAATGGTACATAAATTTAATAAGTACTGGGTTGGTTGGTTTTTTGGGCAGTTACTATATTTTTAAAGATTTATTTACTTTGTGTATATGAGTACACTGTAGCTGTCTTCAGACACCCGAAAAGTTTTTTTCTAGTGATTTCTTAGAAGCACTTCATTAACTATTCCCAGATAATCTGTACTAACTCAAGTATTATTTTCCCTTTTCTTTAAGGATATACTAAATTTCCTCATTGCAATTACACATTTTCAGATTACAATTGTTTCAGGTTAAGCAATATTATTGTGTTTAAACATTGGGTTTTACTACTGTTTACTTGTGTTACTTTTCATAAAACTAATTAAATTTTATTACGTTTACT
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000074472-Zfp872:NM_001033813:3
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact





	

	
Alternative protein isoforms





No structure available

		

			
Features


			

				
Disorder rate (Iupred):
  C1=0.000 A=NA C2=0.022
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
PF0135222=KRAB=PD(0.1=0.0)

							
A:
NA

							
C2:
PF0289210=zf-BED=WD(100=10.4),PF134651=zf-H2C2_2=WD(100=6.5),PF134651=zf-H2C2_2=WD(100=6.2),PF134651=zf-H2C2_2=WD(100=6.5),PF134651=zf-H2C2_2=WD(100=6.2),PF134651=zf-H2C2_2=WD(100=6.2),PF046067=Ogr_Delta=WD(100=11.7),PF134651=zf-H2C2_2=WD(100=6.5),PF134651=zf-H2C2_2=WD(100=6.5),PF134651=zf-H2C2_2=WD(100=6.2),PF134651=zf-H2C2_2=WD(100=6.5),PF134651=zf-H2C2_2=WD(100=6.2),PF134651=zf-H2C2_2=WD(100=6.5)

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000089089





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
NA
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chr19:12465734-12466461 
HsaINT0188206
Human
(hg19)
chr19:12576548-12577275 
ALTERNATIVE
HsaINT0188206
(ZNF709)
Rat
(rn6)
No conservation detected
Cow
(bosTau6)
chr7:14013956-14014337 
LOW PSI
BtaINT0166117
(ZNF791)
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: 
GGCAAGACCAGAGCATTAGGG

				
R: 
AGGGCTTCTCTCCAGTGTGAG

				
Band lengths: 
357-2339

			

		

	





	
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"