Special

MmuINT0178912 @ mm9

Intron Retention

Gene
ENSMUSG00000038535 | Zfp280d
Description
zinc finger protein 280D [Source:MGI Symbol;Acc:MGI:2384583]
Coordinates
chr9:72143782-72146655:+
Coord C1 exon
chr9:72143782-72143842
Coord A exon
chr9:72143843-72146508
Coord C2 exon
chr9:72146509-72146655
Length
2666 bp
Sequences
Splice sites
5' ss Seq
AAGGTAAGT
5' ss Score
11
3' ss Seq
TTGCTTCTTTTAAAAATTAGATA
3' ss Score
4.93
Exon sequences
Seq C1 exon
GTGACAACATATATAAAGTCAGATCTGCAACTTGATGGGAGACAGTTCTTTCAACCAAAAG
Seq A exon
GTAAGTTGCTTCAGTAACTGATACTCATGTGCAGGTGATGTATAATTACATTTTATAATACAGTGTGAGAGATGGTCCCCATCTTAGAACCCTAGAACTGTTGAAATAACAAATGAACTGATAAGTCAAGTAGAAATGAACTATTTTATCTCTTTTAACAGAAATAGCTACTGTTTATGTCAGTATTTTATCAGTTTGTTATATATTATCATATAGATTTCTTCTATGCTTGTGCAAGCATTTATTAAAAATTATAAAAGAATTATAGCTTTTTCTTGACATTCTTTCATATATTAACAATGACAGTCTAAGTGTGTATGTGTGTGAGAGAGAGAGAGAGAGCATACATGCATGTTTATATGCATGTGCTGCATACTATATTAGTTTACTCTGGTTTTCATAACAAATTATCATGAACTAGATGGTTTAATTTGGTAGAAATTATTTTTGGACAGTTCTTTAGGCTAGAAAGTTAGGACCAAAGTATTGCTATGCTTTATATCTTCTGTGGGTTTTGAGATAAAAGCTCTGGGCCTCTTATAAATGGTCAATATTGAACTTGTGACTGATTATAGCCATATTATTAAGAACATGGTGGAATGTTGTCCTAATTTTGAGTCAAAAGTAGAAATGGCTCTCTTTAGTATAATAGAAAATAATACTTAGAAATGATAAAGATATTGTTTAAATTAGAACCTCAGATAATTTCTTTTGTAGTCTCACTATCTTTATGTCTGCACAAGTGCCACTGATGTGCATCTACATGGCCTAGGCAATCATATTCATGGTTATATTAGTTGAGGCCCTTAATGCTGTTTTCCTTCTCGATCTTGCCTCCCTCTGTTCTTACATTTCCTCTTTCTCCATTGCAGCCTGAATTATAAGTGCATATAATTAAAGAGTCACACAGTCTGAAAGGCTTTAATTAGCCTTGCCAAAGTTTCATAAAGTTGTTTGTGTGTATGTATGTGTGTATAGTGTTGCATTATCAATTTATCTAACAGCGTTATATAATTAAAGATGAATGTTCTAACTTTCTTTTAAAAATGTGTTCTTTACAACTTTTTATTTATGTGTATGCGTGTGTCTTGAGTTTATGTCTTGTGTATTGAGTGCTGGAGGAGACTAGAAGAGGACATTGAATTGAACTGGAGCTGGGTGTTGAACTCTGGGTGTTGGGAATAGAACTTGGGTCCTCCAGAAGAGCAGCAAGCACTCTTAATTTTTGGACCATCTCTCTAGTCCTTGTTTTAGCTCTCTTTTTATATATGTATTTATTTTGTTGTTTTTAATAATGTGTAATGGGGGAGGTACTTAAGTTCATGTGTAAGTGCTCACAAATTACAGAGGAGGGTGCCAGATACATTGGGCCATCTGCAATATTCTCTTCACTGCTGAGTAACCTTTCCAGCCTGTTTAATTTTTTGTTTTGTTTTATTTTTAAATTTTTCTCCCCTGCCCAAGACAGGGTTTCTTTGTTAGCCTTGGTTATCTGTCCTGGAACTTACACAGTAGACCAGGACCATGAATTCATGAGTATCACCTGTCTCCCCATTGCTGGAATTAAAGGAATGTACCCCCACCACCCCAACTGTGATCTTAAAGTTAATTTTTTAATCCTTCCTTTGGCTTCCTAGAGAAGTCCTCCTAACATGCTGCTGTCCTGCATCCATACCACTTATTCTCTAGACCTACTGACTTACTCTCTCCTGTGACTTTGTTTTGTATTGAATGTCATGCATGGCCTGTGCACCTTATGTGTTAGTATGTTAGTATTTGTTCATTATTCTCTGTGTGTGTGTATACATGTACATATATGCCAAGGTATATGGGTGGGAAGGGAGGTCAGAGGACAGTTTGTGGGAGTCTGTTCTTTTCCACCAAGTGGGTCTTGAGAATTGAACTCAGATCATGAGGCTCGGCAGCAAATGACTTTATCCACTGAGCCATTTCAGTTTTACTCTGTTCAGACATTATTTCTTTGATGCCTAACCAGTTTCTTTTCTCTACTCTACCTCTTTCTTAGAATCCTTTTAATTTATTTTACTATCTTTTGGTCTTTTATATAGAACACTTTTCTTTGTAAAATTCCTAGTGCTTATTGATTGCTTAATCTACATTTAAGAGAGTGATGGTACCTGATCAGAATTTCTCTATTTTTTACTGCATGCATTTCTTTGATCGATTCCTTTAGGGGAAATGTGTAATTAGCTGCATTTGAGATACACCTGACTCCCTTCTTATGTCTGCTCTCATACCAAATCGCAGCCCCTGCCCTCTTTTTAACTCTGCATTTTCCATTTCTAAAACTGGTTTATTCTAATTTGTTTTTTCATCTGTGGCTTCTTATTCTTCATCTTACCCCTCTTCTCTTTTAAAGATAATGGATAGGATATAATCCTTTTTTTTTTCAGAATTAATTGTTCTAAATGTATGAATAAAATTAATTTTGACTGTATTTTTTACCTGCTCTAAATAAACATTATCTGTCTCACGTCTACTAGTTAATGACGTAGCAGGATCTCAGTTTCTTATTGTTACTATCATGTACTCATCACAGACACCAAGTTAAACATTGTTACTAGGATTATTAAAGTAGATTTCTAATATGCTGCATATAGCAGATACTTTTTAATTAAAAGACAGTTGCTTCTTTTAAAAATTAG
Seq C2 exon
ATAATTTAAAAATGGCAGAACTCTTTATGGAATGTGAAGAAGAGGAGCTAGAGCCATGGCAGAAGAAAGTGAAAGAAGTCGAAGAGGATGATGATGATGAGCCCATCTTTGTTGCAGAGATAGCAAGTTCAAAGCCAGCTATTTCAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000038535-Zfp280d:NM_146224:3
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=0.251
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
NO

							
A:
NA

							
C2:
PF138361=DUF4195=PU(10.2=28.0)

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000096175





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000055943, ENSMUSP00000096175f3841A, ENSMUSP00000096175f3842A, ENSMUSP00000096175f3843A, ENSMUSP00000096175f3844A, ENSMUSP00000096175f3845A, ENSMUSP00000096175f3846A, ENSMUSP00000096175f3847A
  



Associated events






Conservation


Human
(hg38)
chr15:56704268-56707262 
ALTERNATIVE
HsaINT0186742
(ZNF280D)
Human
(hg19)
chr15:56996466-56999460 
ALTERNATIVE
HsaINT0186742
(ZNF280D)
Rat
(rn6)
chr8:78872635-78876352 
ALTERNATIVE
RnoINT0167985
(Zfp280d)
Cow
(bosTau6)
chr10:53731662-53739708 
BtaINT0165191
(ZNF280D)
Chicken
(galGal4)
chr10:7094711-7094921 
HIGH PSI
GgaINT1002101
([1])
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
chr7:52437861-52441647 
LOW PSI
DreINT0181245
(znf280d)
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"