Special

MmuINT0179339 @ mm9

Intron Retention

Gene
ENSMUSG00000070420 | Zfp498
Description
zinc finger protein 498 [Source:MGI Symbol;Acc:MGI:3647079]
Coordinates
chr5:146049163-146052338:+
Coord C1 exon
chr5:146049163-146049286
Coord A exon
chr5:146049287-146051198
Coord C2 exon
chr5:146051199-146052338
Length
1912 bp
Sequences
Splice sites
5' ss Seq
CAGGTAAGA
5' ss Score
10.77
3' ss Seq
TAACCTGCTTTGTCACACAGGTG
3' ss Score
8.43
Exon sequences
Seq C1 exon
GGTCTGGGGCCATTTAAAGACATGACTTTGGGTTTTCCTGAGGAGGAATGGAGGCATGTAGCCCCAGCTCAGATTGACTGCTTTGGAGAATACGTGGACTCACAGGATTGTGGGGTCCTTCCAG
Seq A exon
GTAAGACTTTGCTGGCCAAGGTGAGGGAGAGGAGTTTGGTAGCTGCAGCTTAAGAGTCTTGCCCTAGCCGTGGTGCTGCTGACAGAACAGGGTGGGCATGTGGAGTCTTGGAGAAGCTGGCTTGGTTTGTACATGGCCTAACCACAGGAAGTAGGATGGAGCAAGCAAACACAAGGCGGTGACTGGCGGTGACAGGCAGGTTGTTGATGCCAAGGCAGTGGCTGTGTGCCCATGGCTGAAGGGCATGGAGGGCTGCAGAGAAAGGAAGGAGCAGAAGAGGAGTGTGGATCTGGGCATCCCTGCATGCAGGCCCGAAGGAGCAGCTTTGCTTTGGGACAGGGTGGGAGTGTGGCTGTGCTGGATGGGAGAATGCAGTGTGCCTGCACGTGTGTGCCTGCACGTGTGTGGACAACTGTAGGTAGAGTGAGTGAGGGCTGACTGATGATGTCAGAGGGTTAGTAAGGAGATGATCTGGATAGAAATCACCAAGTTGCATTTGTGTATGTGTGTTGTCTGTGCACACACATATATGGCTGCACACATCTGTGCTCACGCCCAGAGGAAAGAAGAGGGTATCAGGCATTTCCCTTTGTCACTTGGCCTCATTCCTTTGAGGCAGGAGCTCTCTGACAGTCCTAGTGATCTTTCTGTCTCCACCACCCACAGTGCTGGTGTTAAAGTCATGCGTGAGACCACACTAGGCTTGATCTGTGCATGCCGGGATCTGAACTCAGGTCTGGTGGTTGCACAAGTGCTCTTAACCACTGAGCCATCTCTCCAGCCCTACTGAGTTAGATTTTGAAGGAAGTAAAAGTCTGAATTAGCAGGACATTCAGTGGGATGGTATGAAAATCTGTCATGCCGTTCAGCATCAGGACAGGGAGGTGGTGAGAGTAAAGAAAGGTCAGCGTTCAGGGCTCATGGAAGTCAAAGGTGTTGAGGTTGTTAACCAAAGGAAAAGAAGAGGCGCCATTGATGGGACATACTAAGAAGCTGGGTATGATTATATAGGCCTCATTCAGGATTGCATGAGTCTGAGGGCAGCCTGGTTTACAGAGTGAGACTCTATTCCTAAAAGCCAAGATCCCACCACCACCACCAAGATAAAGGGATGCATTTGTAGGCAAAGTCCTAGGACAACAAGTTCCTTAGGTGGCCAGTGATAGAAAGAGAGGAGCTGGTTTTCAGACATGCTCTGCTAGCAGGACCACAGTGTCCCAGTGGGAGAGTGCACCTTTAGAGGGGGGGGGGGTGGCATTAAAGGAGCCATAGATAGCATACTAGTGAAGTGTAGGTCGTATCATAACCATAGGCAGCCTGAAGGTCTTGAGAGGAGAGATAGCAGCCGATAGGTCTTTCAGATCCCCAGAAAGAAGTCACTTTCTGTTTTATGAAGGTTTTGGGGATGTGGTGGTAAGTTTATATTGTGCCTCCTAGCCTAACCTAGTTCACATGGTCCCTGACATGCAGGAAGCCCTGGGTAAGGGTTAATAAGAGGACTTTGGTTCTACCTGCCTCCATGCCTGTGGAAGGAGTTAGGCTTGCTCACATCTGCAAGTGGGAGAGAATTAGGGGCTATAAGGTCAGACAGTGCTCTAGAGTGGTGGTCCTCAACTTGTGGGTTTGAAGTTGAGAATCAGATATCCTTCATATCAGATATTTATTTACATTACGATTTGTAACAGCAAAATTACAGTTCTGAAGGATCAATGAAATAAGTTTGTGGCTAGGGGTCACCATACATTAGGAACTGGGTTAAAGGGCACAGCAGTAGGAAGGTTGAGAACCACTGTCCCAGAGCTGGCAGAGAAACAGGTACAGACTGGGGTGGTGCCTGGTTTCTGGGCATGAAGAGCAGCAATTGGAGGTGTGATGGGACATCACCACAGTGTTAACCTGCTTTGTCACACAG
Seq C2 exon
GTGCTGGGAGCAAGGAGAAGGAGGCTAAGCCCCAGCAGGAAGACCTGAAGAGAGCATTTGTTGGGTTGACTTCCGATGGCTTTGGAGAAGCCGACATCCAGATTCCTGGACCAGGGGGCACCTGTGAGCAGGAGCCTGGGAGCTCTGGGACCAGTCTGCCTGGGCTTCCTGCTCCTCAGCATGGGGTACCCCTGCCTGACACCCTCAACACCCACAATTCTTTCTGGAAGCCTTTCCAGTGCCCTGAGTGTGGAAAAGGCTTTAGTCGGAGCTCCAACCTTGTTAGGCACCAGCGGACCCATGAAGAAGAAAAATCCTTTGGCTGTGTGGAGTGTGGGAAAGGTTTCACCCTGAGGGAATACCTCACCAAGCATCAGAGGACCCACCTGGGCAAGAGGCCCTATGTGTGTGGCGAGTGCTGGAAGACCTTCAGCCAGAGGCATCACCTGGAGGTGCACCAGCGTAGCCACACTGGGGAGAAGCCCTACAAGTGCTCAGACTGCTGGAAGGGCTTCAGCCGGAGGCAGCATCTGCTGGTGCATCGCAGGACGCACACAGGGGAGAAGCCCTACACCTGCGAGTGTGGCAAGAGTTTCAGCCGGAACGCCAACCTGGCAGTGCACCGGCGTGCCCATACTGGGGAGAAGCCCTATGGCTGCCAGGTGTGCGGCAAGCGCTTCAGCAAGGGGGAGCGACTGGTGCGACACCAGAGGATCCACACTGGTGAGAAGCCCTATCACTGCCCAGCCTGCGGCCGCAGCTTCAACCAGAGGTCCATCCTCAACCGTCATCAGAAGACCCAGCATCGCCAGGAGCCTCCGGTGCAGTGAGCCTACTAAGGGAACAGCTCTGCCATAGGAGCGACTTGTGTTGCACCGAGTGGTCTGGGCAGTGCCCAGTGAGGGACAGCAGAACGTGCTCAAGTAGGAGGAGGGCAGAGCCTGGAGTATGTAGGGGAAGCTGGCAGAAGGCCCACAGTTTCCCTCACCTCTTACAGGGAAACACTATCCTGAGCTTCAGGTTTTCTTATCCTTCCTCCCACAGTGGGGATGTGAACCCACCTCCTGAGCAAGTTTAGAGGAAAAGGCAGAATTTTATTGCAAATAGGCAGCTTGAAGCTTGTTTTCTTCTTTCTTTCCC
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000070420-Zfp498:NM_001081431:4
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact





	

	
Alternative protein isoforms





No structure available

		

			
Features


			

				
Disorder rate (Iupred):
  C1=0.381 A=NA C2=0.373
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
PF0135222=KRAB=WD(100=81.0)

							
A:
NA

							
C2:
PF0009621=zf-C2H2=WD(100=8.3),PF134651=zf-H2C2_2=WD(100=9.4),PF134651=zf-H2C2_2=WD(100=9.4),PF134651=zf-H2C2_2=WD(100=9.0),PF134651=zf-H2C2_2=WD(100=9.4),PF134651=zf-H2C2_2=WD(100=9.4)

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000091664





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
NA
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chr7:99624181-99629190 
ALTERNATIVE
HsaINT0187423
(ZSCAN25)
Human
(hg19)
chr7:99221804-99226813 
ALTERNATIVE
HsaINT0187423
(ZNF498)
Rat
(rn6)
chr12:11775969-11777808 
ALTERNATIVE
RnoINT0169486
(Zscan25)
Cow
(bosTau6)
chr25:37343847-37345205 
ALTERNATIVE
BtaINT0166409
(ZSCAN25)
Chicken
(galGal4)
chr1:60057726-60057758 
GgaINT1030719
(ZSCAN2)
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected




Primers PCR

	

		

			
Suggestions for RT-PCR validation

			

				
F: 
TGAGGAGGAATGGAGGCATGT

				
R: 
TTTTCCACACTCAGGGCACTG

				
Band lengths: 
343-2255

			

		

	





	
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"