Special

MmuINT0006617 @ mm9

Intron Retention

Gene
ENSMUSG00000035279 | A430110N23Rik
Description
RIKEN cDNA A430110N23 gene [Source:MGI Symbol;Acc:MGI:3606211]
Coordinates
chr7:4881604-4885054:+
Coord C1 exon
chr7:4881604-4881765
Coord A exon
chr7:4881766-4884736
Coord C2 exon
chr7:4884737-4885054
Length
2971 bp
Sequences
Splice sites
5' ss Seq
CTGGTGAGT
5' ss Score
10.1
3' ss Seq
TTTTTTTTTTCCTATTCCAGGGT
3' ss Score
11.3
Exon sequences
Seq C1 exon
GCATGCCTCTCGGTGCTGTGCAGCCTACAGTTCCTGCAGTGGACAGCAACAGCACAGCACACAGGCTTCTGTCTACCTCCGTGGGTCAGATGCCAGGCCCAGCAGGCCCTTGGCCTCCTTCTGCTTCTCCTACTGCCCCTCCAGAGCCTGGGCCCGAAGCTG
Seq A exon
GTGAGTCCCTCTCTGCCCTAGCTCTAAGACTGTCTCCATGAAACCTGCTTACAAAAAAAAAAGGTAGAAAAGAAGAGCCCAAACCCCTGCTCAGATCAGTACTTGATTAATGCTCTGCTGATAGCCTAAAATCCAGGGTTGCTTGTAAGAGTTCTCCCTTCTGTAGCTGGCCCTGACCTGGAGAGGAGGGTGGGCACGAGAGCCCACTGCCTAACGTCTGGGTTCTGTGGTGGGACTGTTACAGTGTCCTCTGGCTAGCCACTGACTGCTCTTCCAGAGGACCTGAGTTCAATCCCCAGCACCCACATGGTGGCTCACAACCATCCGTAATGGAATCTGATAGTGTACTCATATTAGAAAAAAAAAAGGAATTGTTCTGAGTCAGGCGGTGGTGGCACACACCTTTAATACCAGCACTCTGGAGGCAAAGCAGAGGCAGCTTGGGCTACAGAGTGAGTTCCAGGACAGCCCGGCCTACACAGAGAAACCCTGTCTCAACAAACAAACAAACAAACAAACAAACAAACAAACAAACAATCAGGGCTCAATTGGGTAAGTGCTTAACTTGCAAGCACAAGGATGTGAATTCAGATCCCCAGTAGCCAAATTAAAAAAAACCTAGGTACAGCAGTGGATATGTCTAACTCCAGCACAGGGTGGGAGAGATCCTTGGGGCCTGCTAGCCAGTCAGTCTGGCCAAATCAGTGAGCCTCAAGCTCAGCGAGAGACCCTGTCTCAAAACAACAACAACAACAACAACAACAACAACAACAAACCAAGCTAGAGAATGATGTCAACCTCTGGCTTCCACATGAATGCACACACACGTACATTCACACAAACACAAGTTGTCTCTCAGGACCAGAGGATGGTCCAGTAGGTAAAGGCCACCGAGCCTGATGGCCTGAGTTGATCCCTAGGACTCACACTGTGCAAGGAGATCCCTGACTCTTAAATTTTTCCTCTGACCTTCACATACATGTGGTGGCATACACACACCCTTGTGCATACATACATACACACATAAATAAGTAAATAAATAAATGTAATATTTAAAAACTCCAAAAAATAAGATAAAATAACCCCCTTGGTGCAGTGGGCACGGTACTCCTGCAATTCCAGCAGATGAGAGGCTGAGGCAGGAGGATTATGAATTTGAGCCCAGCCTGGGCTGCACTGTGCATTTCAAAGTGCATTGCAGAGGTCACTACCATGTCCTGTTTACCTGTCGCTACACTAAGGAGCGCCTTTGAATTATTGTGACTAGCACAGCGCAGTGTATGTATACAGCAAGTGACTAGCATAGCACAAGTGTATGTATACAGCAAGTGCATGTATACAGCAAGTGCATGTATACAGCAAGTGTATGTATACAGCAAGTGTATGTATGTATACAGCAAGTGTATGTATGTATACAGCAAGTGCATGTATACAGCAAGTGCATGTATACAGCAAGTGTATGTATACAGCAAGTGTATGCTAACAGACACTTTCAAGTTTTTAGAATCATGTCTATCATGGTACATATCGGTTAGAGTGTAGTGGTACCCGTTCTGTGCTCCTGATTGGTCTCACAATCGCACCACTGGCTGTTGACATCTTTATTTACCAGTTGGATGCAACTGGGGGCCGGGTCCTTCATTGCCTTATGTGCAGATACTTGTGTAAGCAGTTTGAGGGACCAAAATTAATATTATAACACAAGCAGCATTAAGCCAAACTCACTTCATTTCCCCCCTTTCATCTAATTAACAGGGCTCTTTTATCTCAGACATAAATTGAGTACAACTATAAAAATTATGTAAATTACAAAGTATGATGTACAAGTGACATCTGATTCATCATATTTGTCAGTTAGATAAAGTATTCCACCATCTAGCTAAACTCAAAGAGTTTATACTTTTATATCTGAATTATGTTCTGATATTAGCTTGCATTACCATCTGAAAACCATCCTTTCAAATATATATCATCTCTCTCAATGCTAAACAACTTGTGTTTGATTATGAGACTATAACTAGTCTCATAATCCAAGAAAGAAAATCCAAGAAAGAAAGAAATATAACCTGAATATACAGGAAGCACAAAAACATAGCTTCCAAAAACTTAAACAAATTGTGGAGACAGCTGCCTGCCTGGACAGCCCCTAACTTCTTATAACAGATGTCAGAGCATCTGTCTTCCGCTTTCTGGCCCAGAACCATCTGACAGACCTTGAAATAAAGCAGGAATATGAGGGGCTAGCTTACCCTGCCTTGGCAGAGCTTAGCAGTTGACTAGCCCACATCTGTTTGTCCTCTTTGGACAGTATTTTGTCTGCAGATGAATAGGGCAGTTTTTGCTTAGTGGTTACCTTGCCATTACTGGAGCAACTCCATGTGGAGGTGTTGATGCTCAATTTCTTCTTTGAACCATGAAGAGGGTACTGTCAGGAGCAGGCATGTCTCTAGTCAGAATTTCTAATAATAATGAAATGATTAAATGTTAACAGATACATTCAAGTTCTTAAAATCACGTTTCTCTCCGTGCATGCATGTGTGCACACATGCCACAGTACACATAGTGGGAGAACTCTTTTTCTGCCATGTAGATGTCCCACAGGTCAGACTTCTGGTGTCAGGCTTGAGGGCAGGCGCCTTCACCCACTGAGCCATCTCGCCAGCCCCCTTTCAATGTATTTTGGGTGTATCCCTAGGAGTGGGATTTCTATATCATATGGTAATTCTACATTAGCTTTCTGAGGAGCCAGCCAGCTCTGCTTGGCTCTGTGTCCAGTGCAGGAGAGATCTCGATCAGTGCCTGCTACCTGAGCTGAAGGGTTATGAGGAGAAGCAGAGCTGAGGGAGCTGATGGGCATTTAGAAAGGAAGGCAGAAGGCAGGTAGATGAAGGCTCAGAGTGCTAGCTGGGCTCTTTGACCCTGACTCTTGCTTCTTCTTCTTCTTCTTCTTTTTTTTTTTTTCCTATTCCAG
Seq C2 exon
GGTCCCCCCAGTTGCGCCTGGTGGCTGGACCCAGCAGGTGCTCTGGCCGGCTGGAGGTATGGCATGACGGACGCTGGGGGACAGTATGTGATGACAGCTGGGACATGAGAGACTCAGCTGTGGTCTGCCGGGAGCTGGGCTGTGGGAGGCCTCGGCAACCAGACCCCGCAGCAGGCCGCTTTGGCTGGGGTGCAGGCCCCATCTGGCTGGATGACGTAGGTTGTATGGGGACGGAGGCTTCACTGTCAGAATGCCCTGCTGCTTCCTGGGGGAAACACAATTGCGCCCACAATGAGGATGTCGGGGTTACCTGCACTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000035279-A430110N23Rik:NM_173008:8
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact





	

	
ORF disruption upon sequence inclusion





No structure available

		

			
Features


			

				
Disorder rate (Iupred):
  C1=0.873 A=NA C2=0.280
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
NO

							
A:
NA

							
C2:
PF0053013=SRCR=WD(100=92.5)

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000052126





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
NA
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chr19:55494784-55497879 
LOW PSI
HsaINT0159402
(SSC5D)
Human
(hg19)
chr19:56006151-56009246 
LOW PSI
HsaINT0159402
Rat
(rn6)
chr1:72455596-72457227 
LOW PSI
RnoINT0143838
(Ssc5d)
Cow
(bosTau6)
chr18:62465427-62465644 
LOW PSI
BtaINT0141330
(SSC5D)
Chicken
(galGal4)
chrLGE64:656502-657683 
ALTERNATIVE
GgaINT1001348
([1])
Chicken
(galGal3)
chrUn_random:33245740-33245815 
GgaINT0002602
([2])
Zebrafish
(danRer10)
chr4:10952437-10952567 
DreINT0136693
(si:ch211-161n3.4)
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"