Special

MmuINT0046176 @ mm9

Intron Retention

Gene
ENSMUSG00000030160 | D630042F21Rik
Description
RIKEN cDNA D630042F21 gene [Source:MGI Symbol;Acc:MGI:2442838]
Coordinates
chr6:129466593-129469245:+
Coord C1 exon
chr6:129466593-129466759
Coord A exon
chr6:129466760-129467168
Coord C2 exon
chr6:129467169-129469245
Length
409 bp
Sequences
Splice sites
5' ss Seq
CATGTGAGT
5' ss Score
7.83
3' ss Seq
AACTCTGTCTTCCTTCACAGCTC
3' ss Score
11.01
Exon sequences
Seq C1 exon
GTTGCTGGTGGTGGTTGGCGCACTGCTTCTCCTGTGTGGCCTGACTTCAGTATGCTTCCGCTGCTGCCTGAGCCGTCCAGAAAACGGGGAAGATGGGGCCCCGCCGCCTTATGAAGTGACTGTCATTGCTTTTGACCATGACAGCACTCTCCAGAGCACCATTACAT
Seq A exon
GTGAGTGGACTCAGAACACTAAGATAGGGGGTCAGGTTTGAAGATGTACTAAAAGGTTTGGCGGTGCATGTAGGGCAACCTGCCGACTAGCATTGCGTTTGGGAACTCGGTGTGGTTTTCATTTCCAGAATGTGGTGACCTAGGCTGTCACTGATGCCTGAATTCTCAAGGTTTCGTTTGTTGTTGTTTGTTTGTGTTTTTTTTGGCTGATGATAAATTGACCAACAAAGTAAAATATTGGAACAAAAGTTCTTTGAAGGATTTTTGTGAAGTTCGTCAAAGGTCACGGCAACGTGTTTGAACACAGGTGAAAGACAAAGAGACTCTCGGTGTGATGTAGATCTCTCGAATCTGAGGATATCACCTTTGGGTGTGATCATCTCTACACCAACTCTGTCTTCCTTCACAG
Seq C2 exon
CTCTGCAGTCCGTGTTTGGCCCTGCAGCTCGGAGAATCCTGGCAGTGGCTCATGCACACAGCTCCTTGGGCCAGCTGCCTTCCTCTGTGGACACACTCCCAGGCTACGAGGAAGCTCTTCGCATGAGCCGCTTCACAGTCGCAAGGTGTGGGCAGAAAGTTCCTGATTTACCCTCCGTTCCAGAGGAAAAGCAGCTGCCTCCCACGGGGAAGGAATCTCCTGGGACAGAACCCCCATCACACTGATGGGGGTACTGACGGGATTCCTGATAGTCAAAGCATCATCAGACCTGGAACGATCCCAAGATACATGAGATGTTTTCTTTTATACCACCCAGCAAGGTTCAGGATGCCACCTAGACATGTTCTGTGAACAAGGTGGGTTCTCACTCTTCATTCACAACAACGTGCTTTTTCTGATACACACATTGCTAATTGAGTTCTAACTCGTTATTCAAAGTTCAAAGCTTGCAACTCACCTTTAGCTATATTGACTACTACCAAAGCATGGAACATTAAGGTGTCTTGAATTCCTTCAACTACAGCATGCATATAAAGTTTCTTTAACCCTATAATCCTGCAAATTGCTCTTCCCTCTACTTGACTGTGGTAATCTTGAAGGGAGACATACTTTGTGCACAGCCACTACCATCAGTGCACCAAATCCATGCATCTTTCCTTTTAGGGAACAACCACCATTATGCTGAACAACCTGGTACACCATAGAATCCCCACCTGGACTTGCAGATTGCACAGCCAGGGGTTCTGATATGAGTGGAGAGACTATACTACAGTATGTGGCACATGTCAAAACCGTTCTATCAGTTTAGTCTTACCCACAAGAGTGAAACATTGTATAGAGTACAGAAGTGGTCCTAGCAACTTTTCAGTGCTTTGTCCTGCAAACACACACACACACACTCACACACACACACACACACACACTTTTTAGGCTCTGAAAGAAAGCATTCCTCTGCTTCTTTCCTTCTTGTTCTCAGGATGGAAAGCCTTCACCATGTAGTCTAGAGTGACCTATCCTGGCTCTTGAGGTGGGTCTTGCTGCCACCTAGTGGAACAATAATTAAAAATTCACTCCGTTGAGGTCTGTGCACCTTTCCAATTCTCAGTGCTACCCTAACTAAGCCTGGATCTTCTTCTGATGGCATATACAATCAAAAGAGGGTGCCAAGCTATCCTGGTGGTGCCACCTTCCACACTGCTGTCATTACCATCAAAGCAGTGAGATGTATTCTGGGGGAAAAAAAAACTGCTTAGAGAAGTTACTCAAATCCTGGAATAATCATTTTCTCATCTGTAAGTTAGACATCATTGTGCACATTCAAGAACACATATACCCCAAGGCACTATTTGTAAAACATCCCGTGTATCACGTGTTATTCTTCCTGTTGTCCTCTGCTCTTCAGTGGCCTGTGGTAACTTCACTGAGAATTATTTTCTGGTTTGTCCTTTTGCCTGTCTGTCTGCTGTGTTATTGTAAAACCATAGGTAAAGTACCTTTATTTTATCAATAAAAATGTCTTGATTGAGATAAACAGAAAACAACAACAACAACAACAACAACAACAACAACAAAACACCTAAGGATTCCTCTGAACACACTTTGCAGACAAAACTGTTTTGTATGTGACTAGCTGGGGTACCCTGGGGGGATGATTCGATGGGGGAGGGGGCTGATGAGTGCTGCACCTCATTAAATACATTCTTGCAATGTTCACCGAAGCCCTGAGGGAAAAGCACTGCAAGTGAGTGCAATCTGCTAGTGATTGGAACTCCTGAATCACAGATCAGAGTGCCTGGGCAAGCTGATGAGCATAAGTTGTTAGCAGCAGCTAAAACGGTTTTACTTTACCCCCACCAAGAAAGTCATCCACAAAATCGGCTTCACTTTCTCTTCACCTTCAATTATTCATCTTTTCTTTTGAGATGGTACTTTGATGCATAGACTAGGGCAGTCTCCCAGTTTCTATGACACCAAGACTTGCCTTCACCTGCCAATTTCCTGCCTAACTCTGTCTCTTTTATTATTATTATTAAATTATTTTATTTATTTATATTCC
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000030160-D630042F21Rik:NM_001081186:4
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=0.321
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
PF149791=TMEM52=FE(39.4=100)

							
A:
NA

							
C2:
PF149791=TMEM52=PD(45.1=78.0)

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000032263





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
NA
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chr12:10186590-10189895 
ALTERNATIVE
HsaINT0020260
(TMEM52B)
Human
(hg19)
chr12:10339189-10342494 
ALTERNATIVE
HsaINT0020260
(C12orf59)
Rat
(rn6)
chr4:163271828-163272217 
LOW PSI
RnoINT0152906
(Tmem52b)
Cow
(bosTau6)
chr5:100225486-100227253 
BtaINT0150017
(TMEM52B)
Chicken
(galGal4)
chr1:77904351-77904793 
LOW PSI
GgaINT0121812
(TMEM52B)
Chicken
(galGal3)
chr1:81590593-81591035 
LOW PSI
GgaINT0121812
(C12orf59)
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected




Primers PCR

	

		

			
Suggestions for RT-PCR validation

			

				
F: 
CAGAAAACGGGGAAGATGGGG

				
R: 
AATCCCGTCAGTACCCCCATC

				
Band lengths: 
354-763

			

		

	





	
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"