Special

MmuINT0180856 @ mm9

Intron Retention

Gene
ENSMUSG00000050619 | Zscan29
Description
zinc finger SCAN domains 29 [Source:MGI Symbol;Acc:MGI:2139317]
Coordinates
chr2:120991780-120995139:-
Coord C1 exon
chr2:120994935-120995139
Coord A exon
chr2:120992455-120994934
Coord C2 exon
chr2:120991780-120992454
Length
2480 bp
Sequences
Splice sites
5' ss Seq
GCGGTGAGG
5' ss Score
7.93
3' ss Seq
GTTTGTTTCCCTGCAAACAGGAT
3' ss Score
8.42
Exon sequences
Seq C1 exon
GTCACAGTCTCTGTGAAGGGGCAGGAAATGCACTCGGAGAAGATGACACCCCTGAAATCATCACAGGAGTTATTAAGTGTTCTGCAGGAGTCAGTGGAACCCCAGCCCAAGGGTGTATCCAAGAAAGAGAGGGCAAGAAGGCCAGCCCTGAGACTACAGGAGCAGATGAACCCAAAGGAGAATCTCAGACCTTTTCAAAGGAGCG
Seq A exon
GTGAGGAGTAGATGTGTGTGGGAGACAGAGCCCTCTAAGCTGGGAATAGGGTTGGGAGTAGTGAGTGGGGAAGGTTTCAGGGATAGTGGCACCTGTGTGGCACCTCCCAATGTGATGTTTCAGGACCCTGGAAAGGCAGCTAGCTCAACCCTCTGGTAGAGTAAGTATTTTTGTATCTCTTCCTTTGATAAGTCTGCCTAGTTCTCACTATAATCGGAATACTTTTATTTCTGGTGATAGATGCTTATTTTCTAGACCCTCTTCTATACTGAAGACACCTTCATTCTAGTAGTTTTTCTTTCCCTCTGTTCTTTATTCTTTAAATCTAAGTTCTTATTCTCTACATTGGAACCTTGAAGTTCTCTAAATACTTGATTGTGGAGAAGGAAATTATATCTGTGTTATTCTTGCAAGATGTTGTAAAGATGTAAGAATTTTACTTCAGAATTTTGCAACCTCCTGCAGTATAGCCCAGCATTACTACAGAATGGTCTTTGTTCACCTGGTAACACCATGACTCTTAGCTTTCCCCGGTGCCTTTGGATCTAGTCACTTAGTCATTTTGTAGAACTTGTTTTTCTTTTTTGTGCTCTATTGAACTCTATTTTGTTTTTGTTTTTGTTTTTTAAGATTTATTTATTTATAGGTAAGTACACTGTAGCTGTCTTCAGACACTCCAGAAGAGGGAGTCAGATCTCATTACGGATGGTTGTGAGCCACCATGTGGTTGCTGGGATTTGAACTCCAGACCTTCGGAAGAGCAGTCGGGTGCTCTTACCCACTGAGCCATCTCACCAGGCCTGAACTCTATTTTGTTTATTATTATTTAAAACTTAGTGAGGTTGTTTTGAATTCTGATCTTATCATCCAATATGACCAGTAATAGCATTCTTGGTTAGTTTAATAATGGTCTTTAGTCATCCATTGGAAGTACCCCAACCTTGATATAAGGAGCTGCAGAATCAATCTTACTGTGTGCTGCAGGGTACATATACTGCAGTAAGGAAAGGTACCTGTTGGCCAACAAGCTGGCTCAGCTGATAATGGTACTTTCTGCACAGCCTGATAACCTGTGTAGAAGTCCATGAAGTTGTCCTCAACCTCCACGTGCACCATAGCAAGTACACCATAATACGTGCACTGTAGCACGTGCACCCCCACCATATATCATGCATACACGATGAACGTTTTATTAAAGTACCTGTTCTCAAAAAGCTTACAATATGATTTAAGAGCACACAGTGAGCTATGAATATGTACTGAACTCAGCTGTTTGAAAAAAGGGTCAAGTTGCTCAGTTGTCCTGTAGGGGTTTGGTAGTGTGGCCATGAGATGGGGTCCCAGGAAACACCTCCTGAGGGCAATGGCAAGGAAGCTTCCTAAAGGATGGGTGAGTGCCAACAGGAGGAAGGGAGGCACAGAGGTAAATGAGAGTGTACAGTGTTCTTGAGAGAAGAGGAATGGACAGAATATACTAGACACCAAGGTTAAGGCTCAGCAGGACAGCAAGTGAGCTGAGGGGCAGTTAGCACAGCGACTGTTGTGGTGCTAGTTATAGGAAGAGGAAGAGTCTGGACATGAATGGAAAGGAGGACATGCTGAGGGAAACACTGAGAATTTGGTGACTGAGTGTAGAGGACCTTCCCCCCCTCCCAACTAAATTTAATTCTCAGGAGTGAAGTTAAAAAAAAAAAAAAACTAGAAGAGACAGGAATGAGTGACTGAGAAGTGCTAGGATCTGCAAACAAGTGGTGTAGAGGCTAGGGAGCAACCTGGAACGGAAATACCTGCTGGAAACTTACCACAGACCACTTTCTTCTCTTGTTCTGCTTTAGAAGACAAATCAAGCTCTTTCCTATCCTATGAGGTTTCCTGTATTTTCTATTCTTCAACCCATTGAAATTTCTGAAAACATTTCCTTTATAATTTGTTTGTTTGTTTGTTTTTTAAGACAGGGTTTCTCTCTGTAACCCTCACTGTCTTGGAGCTCACTCTGTAGACCAGGCTGGCTCAGAGGTCCACCTGCTTCTGCCTCCTGAGTGCTGGGATTAAAGGTGTGCAGCACTACTGCCTTTCTCCTTTATAATCTTGTAGATAAAAGCTGTGAAAGTAGCTCAGTTTGTAGAATGCAGAACACACAAGGCCTCATTTGATTCCCAGCATTAGATAAAACTCCGCTAGGCATTGCACATGTAATCCCAGCACTGAGGTGGAGGCAGGAAGATCAGAGGTTTAAGGTCATCCTCCACTACATAGCCCCAATCATTGCACATGTAATCCCAGCACTGAGGTGGAGGCAGGAAGATCAGAGGTTTAAGGTCATCCTCCACTACATAGCCCCAATCAGGCTAGTCTGGGCTATATGAAACCCTATTTCAAACAAGAAGATAAAATCTCTTGAATGAAAGAAAGGCTTTTTGTTGTTTGTATGATACTTTGATAACAAACTGTGATACTTTGGTTTGTTTCCCTGCAAACAG
Seq C2 exon
GATTTCCATTTCCTAAACCCAATGTGGTGTCCAGGTTGGATCAAGGAGAGCCATGGATCTCAGATCTGCTTAGCTCCAAGGAGAAGGATGTCCCAAAAGGCAACACAGGAACCAGTCTATTACCATCCAAGAGAGAGAGAACCTGCTGGGTGGAACAGGGTCACTGGGTATTTGATGATGAGAAGGTGGTGGGTGTGCACTGGGGCTACAAAGAGACTAGAACACTCCTTGCAATTCTCAGTCAGACTGAATTTTACGAAGCGCTCCGAAACTGTCACAGGAACAGCCAAGTGTATGGGGCTGTAGCTGGGAGGCTTCGTGAATATGGTTTCCTCCGGACTCTGGAACAGTGTCGGACCAAGTTCAAAGGCCTTCAGAAGAGCTACAGGAAGGTCAAGAGTGGTCATCCACCCGACACCTGCCCCTTCTTTGAAGAGATGGAAGCCCTGATGAGTGCCCAGGTCATTTCATTGCCCATTAATGGCCTGGAAGAGGCAGCCTCCCATTCTGCCCAGGCAGGCAGTGATGCTGAGACGGAGAAGCCAGGGCAGAGGGACTGGCAGCATGAAGATGGAGAGGAGGCTATAGCTGAAAGGTCAGACAGTGATGACCCGGAGGCAACCCCCCAGGACCCTGACAACCCACCTGCACCTGTCCTGTTCCGAAGCCCAAGTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000050619-Zscan29:NM_178889:2
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact





	

	
ORF disruption upon sequence inclusion





No structure available

		

			
Features


			

				
Disorder rate (Iupred):
  C1=0.768 A=NA C2=0.348
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
PF0202312=SCAN=PD(0.1=0.0)

							
A:
NA

							
C2:
PF138371=Myb_DNA-bind_4=WD(100=38.1),PF138371=Myb_DNA-bind_4=PU(0.1=0.0)

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000125987





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000078033, ENSMUSP00000106289
  



Associated events







Other assemblies


mm10




Conservation


Human
(hg38)
chr15:43366809-43368922 
ALTERNATIVE
HsaINT0188829
(ZSCAN29)
Human
(hg19)
chr15:43659007-43661120 
ALTERNATIVE
HsaINT0188829
(ZSCAN29)
Rat
(rn6)
chr3:113127148-113129235 
HIGH PSI
RnoINT0169494
(Zscan29)
Cow
(bosTau6)
chr21:55636256-55638076 
ALTERNATIVE
BtaINT0166415
(ZSCAN29)
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: 
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"