Special

MmuINT0179438 @ mm9

Intron Retention

Gene
ENSMUSG00000078796 | Zfp541
Description
zinc finger protein 541 [Source:MGI Symbol;Acc:MGI:3647699]
Coordinates
chr7:16663321-16667085:+
Coord C1 exon
chr7:16663321-16665175
Coord A exon
chr7:16665176-16667026
Coord C2 exon
chr7:16667027-16667085
Length
1851 bp
Sequences
Splice sites
5' ss Seq
CAGGTATTT
5' ss Score
7.51
3' ss Seq
AGATATCTTCTCATCTCCAGGGT
3' ss Score
7.22
Exon sequences
Seq C1 exon
GACTGGGCACATGCTCACCCACCAGAAGACCAAGCCCTTTGTGTGCATTGAGCAAGGTTGCAGCAAGAGCTACTGTGACTACCGCTCGCTGCGCCGCCACTATGAAGTCCAGCATGGAGTATGCATCCTGAAGGAGACTCCACCAGAAGAGGAGGCCTATGGGGACCCAACTCACAACCATGATGTGGCTAACCAGCCTCCACCCAGTGGCCTGAGGTCCCTGGGGCCCCCAGAAGCTAGGTCCCCTGGCTCTGTCTTGCCCAACAGAGACCTCCTTCGCTGTATTGTGAGCAGCATCGTCCACCAGAAGATTCCTTCTCCTGGCCCAGCAGTGGGGCCTTCTGATACTGAAGCAAGGAGCTCAGCCTGTGCTTGCCCCACCTCACTGGGATCATCATCATGTACACCAGCCAGCACCCCAGTGGCCCTAGGAACCCTGGGCTCTGAGATTCCTGAGGAAACTCATCCCCCACGGAAGGAAGCTGCCACCGAAGTGTTCACACCTGTCCAGTCAAGGGCAGCTGAGAATGGTGTCCCCGATCCACCAGAGTCAGAGTTGGAGTCAGAGTCTCCACGGCTTCAACGGCCATCCTCCCTGGAAGGCTGGCCAGAGGGCAGCTCTCTGCCTGCCTGCCTGCCTCTCTTCAGAGGCCACTCTGTCCCCTCAGGATCCCAGCCTTCCAGCCACAACTTCCAGTGGCTCCGGAACCTGCCTGGCTGTCCCAAGAACAAAGGCAGCAATGTGTTTATGGTCCACAAGCCCCCTGCAGTGGCATCCCGGGAGGGCTCTGAGGGAGGAGGCTCTGGACCCAGCAGCACCCCTACCTCAGTGGAGCCTTCACCCAGCCTGGGCACCACCCAGGAGGAACTCTTGCCATTTCCTCCTGCACTACTAAAGGCCCCTGGTGAGGCCTCCAGTGAAGTTCGGCAGGCAGCTGGGGAAGATGAAACCTGGGCTCCCAAAAAGTGCAAACCTGACTGTGAGTCATTCCCATGGCAGAGCCCCACTGAGCTTGGGCTCCAAGATGCACAGAACCCAGGTGGGCTCCCCTCAGATGCCACGCCCCTCTTCCGGCAGCTGTTCATGAAGTCACAGGAGTCTCTAGTAAGCCATGAGCAGATGCAGGTGCTCCAGATGATTGCCAAGTCCCAGCGGATCTTCTCCCATACTCAGGTGGCTACAGCCTCAGCCCAGAGACCAGGGCCCGAGGGCAAGCAGTCCACTCTGAAGCCATTGCAGGGGCCATGGCCACCACAAACTCTGCCACCAGCACCCACTGTAGACTCTTTCCAGATAGGCCCTGGACACTCAGAGCCAGAAGGATCCCCAGTCCGCAGGAGGAAAACTATGCCTGCGGTGTCCAGAGAAACATCTCCTGGTGGCCCTAGGCGAGACACAAAAGGAGGCCCCAAAGTGGCCTCTGCACCACCATCCCTCACAGGGCCAGGCCTGCTCCCCTCCCGGAATCCAGACAGCTCTTCATTGGCCAAAGGGACATTGGACCTGGGGGACATTATCCCCAATGCAGGCTCAAGGCAGTCCCAGTTAGGTGGAGATGAGCCAGCTGGAACCCAGCTGGTTGGGAAACAGGGGCAAGGAGAAAATGGCCTGGCTTCAGGGGCCATGAGAGGTGAGAAGGGTCCAGCCTGCCCCCGAGGTGGAGGCTACAGGCTCTTCTCAGGGCACCCCAGGGCCCAGAGATTCTCAGGTTTCCGGAAGGAGAAAGTGAAGATGGATGTGTGCTGTGCAGCTTCTCCCAGCCAGGTGGCCATGGCCTCCTTTTCATCGGCTGGGCCTCTGGCAGATCCACCCAGAGACATGAAGTCCAAGCTGACAATCTTCAACAGAATCCAG
Seq A exon
GTATTTGTAGTCCTCTATTGTGTTCTGGGCTGTGGCAGGGCTATGTGTATGTCCTTGGATTTATAGCATTGGTTAACTGTCCAGGTACTTCCCTCACTGTAGTAGGTCTTCAGATGTGACTTTATAAGAGGCACTGATGGCTGTTGTCTACTAAGCTACCTTCCTTGCTTTCCTTTGCCTCCTAATTCCACCTAGATTCCCCTCCTTCAACTCTTGAGCAAGATAAAGGTACAGGCCTCCTCCCTTAACTGTTAACTACATGTGATGGCTGTGCATTCCCCACACGTGCACAGAACCCAAGTCCTTTGTGCATCATGCAGTGACCATCTGCTCTGGGCACTTAGCCACTCCTCTTAGTGAAACCAGCATCATTCCTTCCATCTCACAGCTACCACTTTATAAACATTTACATCTTTGTTAGCCAAATGATGTATAATGAACCCTTACAAAGTTGGAGCTTTGGCAGACATTGGTATAGTCACAAGTTTACACAACTATTACTGTTGGCCAGAAAACTTTATCACTCCAAGAAGATACCCTGCATCCCTTAGTAATCACCCCAGTCTTTTGCTCCTTCTACCATTATCCTTTCAGCCCTGGGTACCCACAAATCCTGTCTCCATTGGCTTAACTGCTCTGGACATTTCATGTCAGTAGAGTCAGATGTCTGTGTCTGGCATTGCCTGTTTGTACCACATGATTAAGGTCCATTCATATGGCACCATCTGTCAGTGCTTCATTTTTTTGTAAGAAATTAAAACAATTTTTACATTTATTTAGACTCAGGGTATGTGACTTTAACTGACCTGGGACTTGCTATATAGTCCAGGTTGGCCTTGAATTCACAGAGTTGAGTTGAGATCAGCCTGCCTCTGCCTCCCCCGAGTGCTGGAATTAAAGATCTGTTCCATCTGGCACATTTTTTGTTGGGGGTGGGTATTAGCATGATCATGAGCGGTCCACAGAGGTCACGTGGGACTCAGAGGGCAGCCTGTGGGAGCTGGTTTTCTCCTTTCATCTGATTGGCAGCAAGTGCCTCTTCCTCCCTCCCCCCATTTTGCTACCTACCCTACTCCATTCCTTTTTCTGGCTGAGCAATGTCCCGTGGGTAGACAGGCCAGATTTTATTTTGCCATTCATCAGTGGACTATTTCCACTGTGGCTCATGTGAGTGGCTACTGGGAAGCTGTGTACAGCTTCTTTCTTGTGGATGCATGTTCTTGTTTCTCTTGGCTAGACCCAAGGCCTGGAATCACCGGATCCTAGAGTCTCGTGCTCAGTGCTTAAGGAGTACAGACTACTTTCTAGGAAGCAGCCGCTTTCCAGTGCCGCTGCTGTACACAAGTGCCCTGTTTCTCCATGCGCTGTGCTGTCACAGTCACACTGTCACAGTCACACTGGGCCATGCAGTGCTGTCTGCTGCTGCTGCCAATGGCGTGCCCTGGCATTAGAATCCTCCCGTGTGCTTATAGACCACTTGTGAAGTGGTGTCTTACTGACTTGCATATATATGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTATGTGTGTGTGTATACACATACATACATACATACATATGTATATATATTCTGTATGTACATCAGACATGTGACTTTATCTTCCCTTGTGTGGGCTGCCTTTTCATCTTATGTGTGAATATTTGTGGGATTGAAGCTTTTAATTTTAATGAGTCCAGTGTGTCTGTTGGGTTTTCTGCTTTGCTTTGGTGTCAAATCTGAGACACCATTGCCCAGAGCACCATCAAGCAGACTTCCCCAATGCTGTCTTCCTTGTTCCTTTGTCTGGGCTTTGCTGGCTCAGATATCTTCTCATCTCCAG
Seq C2 exon
GGTGGAAACATTTACAGACTCCCCCATCCAGTGAAGGAAGAGAGCTTGGCAGGCGGATG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000078796-Zfp541:NM_001099277:3
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact





	

	
No protein impact description available





No structure available

		

			
Features


			

				
Disorder rate (Iupred):
  C1=0.815 A=NA C2=0.500
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
PF0009621=zf-C2H2=PD(30.4=1.1)

							
A:
NA

							
C2:
NO

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000104149





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000131838
  



Associated events






Conservation


Human
(hg38)
chr19:47540952-47544125 
ALTERNATIVE
HsaINT0187578
(ZNF541)
Human
(hg19)
chr19:48044209-48047382 
HsaINT0187578
(ZNF541)
Rat
(rn6)
No conservation detected
Cow
(bosTau6)
chr18:54943212-54945378 
LOW PSI
BtaINT0165691
(ZNF541)
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
chrUn_random:734361-734624 
ALTERNATIVE
GgaINT0002388
(ZNF541)
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected




Primers PCR

	

		

			
Suggestions for RT-PCR validation

			

				
F: 
GCAGTCCCAGTTAGGTGGAGA

				
R: 
CTTCACTGGATGGGGGAGTCT

				
Band lengths: 
355-2206

			

		

	





	
Functional annotations
(Submit an annotation)

	


There are 0 annotated functions for this event 


		










GENOMIC CONTEXT[edit]












INCLUSION PATTERN[edit]










Retrieved from "https://vastdb.crg.eu/wiki/Special:VastDB"