Special

MmuINT0162921 @ mm9

Intron Retention

Gene
ENSMUSG00000028364 | Tnc
Description
tenascin C [Source:MGI Symbol;Acc:MGI:101922]
Coordinates
chr4:63628251-63631478:-
Coord C1 exon
chr4:63631348-63631478
Coord A exon
chr4:63628384-63631347
Coord C2 exon
chr4:63628251-63628383
Length
2964 bp
Sequences
Splice sites
5' ss Seq
AAGGTATCT
5' ss Score
7.56
3' ss Seq
ATTCTTTTGCCTGCCCACAGGAA
3' ss Score
11.35
Exon sequences
Seq C1 exon
ACCTCGATTCCCCAAGAGAATTTACAGCTACAGAGGTTCAGTCAGAAACTGCCCTCCTTACCTGGAGACCTCCCCGAGCATCGGTCACTGGATACCTCCTGGTCTATGAATCTGTGGATGGTACAGTCAAG
Seq A exon
GTATCTATAAATCACACATTGCTGGGTAAAACATTTGATGTGCATAATCATCAAAGTAGCAAAGGATTCGCTGATACTGTTTCTTCACTCCAATACAACTAAACACCTAAAACAAACAAAAAACTAGTAGAGACTGGATATAGAACCAGACCTTGTGAGTCACAAACCACATGCTCACTAATCTTTCTTCCTTTAACCAGGCTCAAGCTATCTGAGCAACAGCCAAGATCAACGGCAGTGCTTTATAAGACTTAACATTTTAAGAGTTGGGCTCATGGCCATCTAATGTTTCATTGAGAAAGTACCAACAGCCTTTTCTGCATCTTTGCCACGTAGTGTCACCACCTGACTGACTGTGATCTATCTCAACACATCCTTGCAATGTCACTTGTTAAGACCAGCTACTTCTATTGCTAATATTACCTGTGTTCTCCCCTCCATGAACTTTACTGTATTTCTAAGCTAGGTTACTTATTCTCTTCATACTTAGCTATATGCAGCATCTCCCCTATATTTTTTATTAGATATTTTCTTCATTTACATTTCAAATGCTATCCCAAAAGTCCCCTATACCCTCCCCCCACCATGCTCCCCTACCCACTCACTCCCACTTCTTGGCCCTGGCGTTCCCCTGTACTGGGGCATATAGACAAGGGATCTCGCCTATATTCTGTGTAGCTACTTCACTTTTGCTCAGAAATACATGTCACTGCTATTGTAGTCTATAGCTCGGGAATTATGTTTCTTCTAGATCACATTAGTTTTGTTGCTGTGGTTTGGGTTAGTTTCCACTGTCCATGCTAGAAACTTCTTCCCAGTGTCTTTTAGTCCTGGCTTATCCTTTCATACTTATGCCAAGAACAAAGAATCTGATTAGAAGCTCAGCTGAACATAAGGGTTTGTTGACACTGGGGTTCAATGTAGAGATCAGCTGCTGTGTACCTGGAAATTTGTGGGGGAACCCCATAGTGCTTAGGCTCTTATTCTATGCAAGCTTTGCTTGCTCTTACACTTCCAGTGTAGTATCTTGACCTCCTCACCAGCTGATCCTGGTGGATTTGAATTCAGAGCCTCCACTGTAATGCAGATTGCTCTGTTCCTTGAGGGGACAAGGAGAATGGGGAATCAAGCTATTCCTCGTGCAAAGCTTCTAAACTGACTGAACCTCTCTTGAGTCACACACTACATTGCCTGCAAAGGCAGCTATGCTGTTATACACATGCATCAGAAACTCGCTGAGTGCTTCCTTGTATGTCAGCCAGCCTGGGGTAGTTCTGCCCACTCCAGGTGGTTCCTAGCACTTTCTGCTCTGGCACTGCAGGAATTGTTCCCTCTACTATACACCTTCTGCCCAGCAAGGTACATAGGAGCTACCTGTTTCTATCTCTTCCTCCCTCCCATTCACTTTTGTAGTTTCATTTCTTCTGGTCCACTCCTGTTTTATAAGATATGAAAAACACATAGAGAAATATTGGTATTTCTGATCTGCCATGTTTAACCACAAGTAGACACATTTCTAGCTTTTCTGGAGTTGAGACAGAACTCATAGTATGAACTGAAGCTGGTCCTTTATTGTCATGGTGTCAGTGCCCATACCTTTAAGATACGAGCATTGCACTTCTAGACCCCAAAAGTCTTCTGCAGGTTTGAGGTTCTAGGATTGTGCTTCCCTGGTTCATAAACCTCATTTCAGACTATCCAGACTTAGACAAATGAACACAGAAGCAGAGAGCTGATTGCCAGTCTAGGCTCAGGCAATTCAATAAACCTTGCTTTGTTCCCTGAGAGTTGATCCTTCCCCAGAAACCAGAGCTGATGGCACCACAAAGGTCACTAGGTCACTGGCATTGAGTGAACACACATAAATCATGGATAAGGTGGTGGGAGACTAGGAGGACGTGACACTGTCCTCTGCCATCAACAAATTATGGATTGGGAGCAAGTATCTTAGCTTCTGGGAAATTCAATTCCCACACTGTAAAAACATACATAACATACCCTCACTCCAGGAAGTCCCTAGGAAGGGAAATAACCTTCCAGTGGCCTCCACTCTGACCTGTTATTGACTAAACCCAATGAACTTGGTGAGTTCTAGAGATCAGAATTGTGTTTGCCGTGATGGAGGAGGAATTCCAGTCTCAAACACCAAGGCCATCTATTAATAAGAACTGGAGCCCAGTATGGATCTGAGGCAATGTGGATCTTGTAGAAACTGAGCCCAAACACTAGTCTAGAACCCAGGGACGAGCCATAAGCATAGTAGGGCTCACACATCTGTTCCTCCCGGGTCAGCTCAAGTCTTTATCCTGCCCCACGCACTAGGCTATTAACGTCATCTTGCAACTCAAGAGTTCCTCGACCTGAGTTTTAGTTTCCCTAGAGATACGTCTGCCTCCCCACCTTCTGAAAATTCAGTGAGTCTACACTGAGGCCCAGGTTATCAGACTGTTTAAATGTTGTGATAAAGGCTAAGCCCCCTTTCAGAACTGCTGACACAAATGGTCTCAGTGTCTCTTGCCCCTTGTGCAATTCACCTTACCATCAGCTTAAGCTTCTTAAGCCTCAACAGCTTAATCCTGTTCAAAACCTCTCAGACCTCCCAACTCCTTGTTGTTGATAAACGCCAAGCCAGTCAAGCCAAAGTGCGTAACATCCCATTAATGGTGTCCTGTAATCCCTCTTTGCCCATTTCTATTACCCACCCCCACCTAAAATTAAGTAGAACTAATGCAAAGCAGTGCTTCTGTGTTATTTAACCCCCCTGCCTTTCTCATCCCAGAGCTTTTACTTATGCAGCACTCTTGCTATCTCAGACATTCCAGAGGTACACTTGGAATCTGGCATGCAGTAGGTGCTGGGTGGGGTTTTATGTTAAGTGAATAAATGATTGCATTAGCCAGTGAGAGGAAGCATCTTTGCCGTGAGACTATCTGGGACCAAACTGATTCTTTTGCCTGCCCACAG
Seq C2 exon
GAAGTCATTGTGGGGCCTGACACCACCTCCTACAGCCTGGCAGACCTGAGCCCATCCACCCACTACTCAGCAAGGATCCAGGCATTGAGTGGGTCCCTGAGGAGCAAGCTGATCCAAACCATCTTCACAACAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000028364-Tnc:NM_011607:19
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact





	

	
ORF disruption upon sequence inclusion





No structure available

		

			
Features


			

				
Disorder rate (Iupred):
  C1=0.068 A=NA C2=0.000
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
PF0004116=fn3=PU(52.6=93.2)

							
A:
NA

							
C2:
PF0004116=fn3=PD(44.9=77.8)

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000102995





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000030056, ENSMUSP00000102997, ENSMUSP00000102998, ENSMUSP00000103000
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chr9:115031686-115035203 
LOW PSI
HsaINT0169921
(TNC)
Human
(hg19)
chr9:117793965-117797482 
LOW PSI
HsaINT0169921
(TNC)
Rat
(rn6)
chr5:79797085-79799943 
LOW PSI
RnoINT0153593
(Tnc)
Cow
(bosTau6)
chr8:105978239-105982710 
LOW PSI
BtaINT0150618
(TNC)
Chicken
(galGal4)
chr17:2646185-2646698 
LOW PSI
GgaINT0124482
(TNC)
Chicken
(galGal3)
chr17:3041004-3041517 
LOW PSI
GgaINT0124482
(TNC)
Zebrafish
(danRer10)
chr5:5229708-5234410 
LOW PSI
DreINT0021387
(TNC (2 of 2))
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"