Special

MmuINT0167065 @ mm9

Intron Retention

Gene
ENSMUSG00000034848 | Ttc21b
Description
tetratricopeptide repeat domain 21B [Source:MGI Symbol;Acc:MGI:1920918]
Coordinates
chr2:66035725-66039341:-
Coord C1 exon
chr2:66039180-66039341
Coord A exon
chr2:66035921-66039179
Coord C2 exon
chr2:66035725-66035920
Length
3259 bp
Sequences
Splice sites
5' ss Seq
GGGGTGAGT
5' ss Score
7.93
3' ss Seq
TTTATCCTTCCTGTCCACAGCAC
3' ss Score
10.69
Exon sequences
Seq C1 exon
GTATACTGGAGAACCAAATGATGCCCTTCGACATTTTAATAAAGCTCGGAAAGATAGTGACTGGGGTCAGAATGCACTTTATAATATGATAGAAATCTGCCTAAATCCAGACAATGAAACTATTGGAGGTGAAGTGTTTGAAAACCTGAATGGAGACCTGGG
Seq A exon
GTGAGTAGCATTTTACACAGTTCTTTAGGAACAGTTTTTAAAACATACATTGGGGAAAATACGCAGGAAAGCACAAGAAAGTCACCTTCTAGCATAATGCTGAGGGAAAAATGGATTGAATATTGTATGAATATATTTATGCTTAATATATATACAGAGAGACTAATGATTCTCCATCTCAGTGTGCTTGTGTGAACACGAGTAGCTTCCATAGATTCACAGATTTGAATCTTTGCTCCCCAGTTGGTAGAACTGTTTGGGAAGTGTCTTAGTCAGGGTTTCTATTCCTAGACAAAACATCATGACCCAGAAACAAGCTGGGGAGGAAAGGGTTTATTCAGCTTACACTTCCCTGTTGCTGCTCATCACCAAAGGAAGTAAAGACTGGAACTCAAGCAAGTCAGGAAGCAGGAGCTGATGCAGAGGCCATGGAGGGATGTTCTTTACTGGCTTGCCTCCCCCGGCTTGCTAGGCCTGCTCTTTTATAGAACCCAAGACTATCAGCCCAGGGATGGCACCACCCAAAAGGGGCCCTCCCTGCTTGATCACTAATTGAGAAAATGCCCCACAGCTGGATCTCATGGAGGCACTTCCCCAAATGAAACTCCTTTCTCTGTGATAACTCCAGCTGTGTCAATTTAACACAAAATTCGCCAGTACAGGAAGGGTTATATGGTCTGGCCTTGCTGGAGGAAGTATGTCACTCAGGGGGGGCTTTGTGGTTTTAAAAAGCCTGGGAAAGTCCCAGAGCTCCCTCTCGGCTCGGCCCTATGGTTGTGAAACAATATGTGAGGTCTCAGCTTACCTTTGCTGTGTCATCACAGACTTTAACACTCTGAAAAACATAAGCCAAATTAAACAGCTTATTTTTTTAAGTTGTCCTGGCCATGGTGTTTTATCACAACAATAAAAAAATAACTAAAACAATTAGGCATGAAATGTTTTCCATTTCCTAAATCATAATAAATGGATTACAAAGGTATTTCCCTAATTACTCTGTCAAAAATAAAATAAATTGCAGAGTCTGAAAAGCATAATACAGACTATCCACATAATATTAGCAATGGCTGACACTTGGGAGATGCCTCAGTAGACAGAGTGCTTGTCCCACAAGTATGAGTACTTGAGTTCAAATCTCCGAGCCTACATAAATGGTCTGTGGGCTTGGTGGCTGGTCTGTCACTCAGTGGCCAGAGACAGAGGCTCTGCACAGCAAGGTGACTTGGTAGACAGCTGTAAAGGCAAACTCTGGGCATGAGAGAGCCTACCTTAACAAATACAGTAGAGTGATTGAAGAATGTTCCTGATGTCAGCCTTAGGCTTCCAATTGAGCACATGCAAAATGTATGCATACACACATGCACAGCCACACAAAACCAAAATGAAGACAAGGGTAAGAGTGCCAACCTAATACAACAAAGTAGCTTTATGCCAGCCCTATGCTCTGCTCTTTTTTGGTTTTTTGAGACAGGGTTTCTCTGTGCAGCACTGGCTGTCCTGGAACTCACTCTGTAGACCAGGCTGGCCTCGAACTCAGAAATCCGCCTGCCTCTGCCTCACAAGTGCTGGGATTAAAGGCGTGCGCCATCACTGCCTGGTGATCTGTTCTTTATACATAACTCTAACTGGCTTTCTGCAACAGCATTGTGAAGTAAGCTCAGAGTTCCTTATCTGAGAAAAGATAGAACAAGGCACAGATAAAGTGCTAGCAGACCCCACAGTTCTTCAGTGTTCACTGTGGGTTACTGCTGGAAAATGGTGCCATCCCCTCAAGCTGTGTCTGTTGTTCCTCTCCCAGAAGAAGTGAGCATAGATGAAGATTCAAAGGGTGTGTAACAGGCAGTGATTGCCTTTCATTAGCATGTGATCCATTTTTAATGCTAGCTGCTCTGAGGCCATTCAGTTGCCACACCACAAATAGTGATCTGAAAGGGTGCTCTTGTTCCGTGCTGCAGGAGGGCACAGGCATGCAGTGCATAGCTGTCAGCAGATGGTGCAAGGAGTGGAGGGACATTGGAACAAGGAAGAACAAACCTCAAGATTGGATTAGCGAGACCAGTGAAACTCAAGTAGAGAAATGACCCGTGTGTTTTAGGAAGGTTAAGATAATATACTATTTTATACCTTTGGACGCTTCAACTAAATACTTGGAAATACAAACTAGAACTCCGGGGAGGAGCTGCTAGTACTCATAGAGATAATGGGAGACACCTGAAAGAGTTGGATCTGTGTGAAGAGCCTCTTTGCAAGTTGTTATATGTAACCACAGGAAACAGACTAGATTTGGGGCATGCTAAGGCTAGAGCTCTCAAGGTCAAAAATGAAAATCAAATTGTACAATCATGAAAGCCAAAGCATACACACAAATGGTGTGTAACAAGCAGTGGCTACCTTTCAACAGAGAATATGGCAAGATCAAAAGGTGTTTGCAGTAAGATTAAAATCACTAGGGCCTGTGCCAGATGACCCAGTGGTTAAGAAAAGCAGATCTGAGATTGGTTTATTACCCACATTGGTTGGCTCACAACTGCCTATAACTCTAGCTCCATGGGGACATCTATCACTCTGCACTGTAGGGAACTTGCTATCAAATATTTGAATTTTTACTATGCCTGAAATTTGCTATCTTATATCGCATGTAGTTTCCTCTCTAAGTGTCTTGTGTAACAAGATAAAGGAAAGAGATTTTGTATGTTTGATAAACTTAGACTCAAATGAGTGTTTTCTATTTGTGATCTTTGAGAAATGATTCTACTTTCTGACTCTCAGTCTTCCAAAATTGGAAGGTATATACACCATACACACCATATACAGAAGAAACATACACTGAAGGAGATCCTACAGCGTCTGGCCCCTTTCTTCTCTTTCCTCGTCTCTTGTCTGTTCTAAGCATTGAACACTATTGGACAGTATCATGAGTCTCCTTAGAATTTTTCTTCCTTTTTGTGGAGCTAGGCACTGAACCCAGGACATCACCTACACTAGCCTATGAAGAGTATATTTTTAATTCTGGTTAGATGTTAGCTAACGTTAACATGTTCACCATGTAGAGATACTGTCTACTTTTCATTTTACCGTGACTTGGGATTTAATGGTGTCTTACTGAGGACATACTGATTTGGTTAAGATTCACTTACGCCACATCCTTGGTATTGGAAGAGTGAGAACACTGATCCTCACGGGAAGTCTTTAATGAATGATAAAAAGGAGCTGCTGCCTTGAGGGACAGACACATGCTGTTTATCCTTCCTGTCCACAG
Seq C2 exon
CACTTCCCCTGAGAAGCAGGAGTCTGTGCAGTTAGCAGTGAGGACAGCAGAAAAGCTCCTTAAGGAACTGAAGCCTCAGACCGTCCAGGGCCGCCTGCAACTCCGCATAATGGAAAACTGCTGCTTGATGGCCACCAAGCAGAAGTCCAGTGTGGAGCAGGCACTGAACACCTTCACCGAAATCGCAGCCTCCGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000034848-Ttc21b:NM_001047604:24
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact





	

	
ORF disruption upon sequence inclusion





No structure available

		

			
Features


			

				
Disorder rate (Iupred):
  C1=0.164 A=NA C2=0.088
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
NO

							
A:
NA

							
C2:
NO

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000099779





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
ENSMUSP00000131758
  



Associated events






Other assemblies


mm10




Conservation


Human
(hg38)
chr2:165888475-165890478 
LOW PSI
HsaINT0174188
(TTC21B)
Human
(hg19)
chr2:166744985-166746988 
LOW PSI
HsaINT0174188
(TTC21B)
Rat
(rn6)
chr3:52299284-52302177 
LOW PSI
RnoINT0157592
(Ttc21b)
Cow
(bosTau6)
chr2:30503690-30505989 
LOW PSI
BtaINT0154320
(TTC21B)
Chicken
(galGal4)
chr7:19179526-19179948 
ALTERNATIVE
GgaINT0048255
(TTC21B)
Chicken
(galGal3)
chr7:21156285-21156707 
ALTERNATIVE
GgaINT0048255
(TTC21B)
Zebrafish
(danRer10)
chr9:50118202-50119477 
ALTERNATIVE
DreINT0169090
(ttc21b)
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"