Special

MmuINT0024346 @ mm9

Intron Retention

Gene
ENSMUSG00000028121 | Bcar3
Description
breast cancer anti-estrogen resistance 3 [Source:MGI Symbol;Acc:MGI:1352501]
Coordinates
chr3:122207845-122211489:+
Coord C1 exon
chr3:122207845-122207973
Coord A exon
chr3:122207974-122211043
Coord C2 exon
chr3:122211044-122211489
Length
3070 bp
Sequences
Splice sites
5' ss Seq
CAGGTATGC
5' ss Score
9.37
3' ss Seq
ATTCACCATTTTGACTACAGGTG
3' ss Score
6.6
Exon sequences
Seq C1 exon
TTCTCCAAGGAGAGGCACATCATGGACAGGACCCCTGAGAGGCTGAAAAAGGAATTGGAGGAGGAGCTGCTGCTGAGCAGCGAAGACCTACGCAGCCACGCCTGGTACCACGGCCGGATCCCCCGACAG
Seq A exon
GTATGCGCTCTGCTCTGTTCCCCTCAGGGACGCGCACACTGATGGCTCTGTTGAGTCCTGCTCAAAGACCACAGAACGCTAGTGCTAGAAAGTGACTTAACTTAGAACCGTCTCTAAAGAGACCTTTGGAAGAACCAAAGGTCGGACTCCAAATATATTTCCAGCCATGAGGGAAAGGACAGTGCTCCTTGGGGTCCACATACATGCGCAGAACCAGCTGCCAGAAGTACCTAGATGCCTGGAGTTCAGAAAATTAAGCTCTTGGCCAGTGGTCAGAGCCTCCTACTACTTGGACCCTTTTCTGAAGGCAGTGACTTATCTCAGAGAAGTTCCTGTGCCACAGGGTAGGAGACACAGACTGACAAAGCCACCCCTGCTTCAATGGGGCAAGCGAGTGTCCACTGTCTTCTGTCCTTCTTCACTGAGTCCTGTGACCCAAAAGATGGGAAGGAAGGGGGATTAGCCCAGGGACCAGGCTCATCCTTCACGGCTCAGGAGATTACACGTAGTTGTGATAAGTCATGTTGCTATTTGATACTGTAAGAATTAAAAATAGACTGAGTCTGCAGAATTGAAGTGTAAAGTTACCCATGGGATTTTATTATAAGCATAACTGGCCAGTCATTAATCAAGATCAGCATAACAGGAAATGCATGCCTAGGTCTAAGGCGGGTGGCGGCATGTTGTAAATACTGTCTTTAGTGTAACGAATTTCACTTTTTAAAATTATTATTTCGTGCTGGGCGGTGGTGGCGCACACCAGCACTTGGGAGGCAGAGGCAGGTGGATTTCTGAGTTCAAGGCCAGCCTGTTCTATGGAGTGAGTTTCAGGACAGCCAAGACTACACAGAGAAACCCTGTCTCAAAAACAAAAACAAAAAAATTATTATTTTGTTTATTTATTTATTGCGGGTGTGTGGAGTGTGCCACAGCACACAGGTGGATATCGAAAGACAACTCTCTTTCCGCCACGTGAGACTCAGGGATCTGAACTCAAGCCATTAGGCTTGGCAACAACCGCCTTTACCTGCTAAGCCACCTTACCAGCCCTATTTTTTTTTTTTAACACTTATCAAAGAAATCATTTTTATTCTGATCTTGAGATAATTTTTTTAACCTTAAAACTGATGGTAGAAGATCCAGATAAGAAAAGAGAAAATCTAACTCCTATCCCTAATTGTCTCCCCTGGAGGTAGTTGTTATGAGCATTCTCGTGCATATCCCTCCAGACCTCTTCAATCAAAACAGAGATCTTCCTGCTTTCTGTGGCCCACTCGCCTCACTTAATGGTGTGCCCTGGGAATTGGCTCCGGCTGTAAACTCTTTGGCTGCCCCAGCACACACTGTGTATATATATGGCTTTCACATACACACACATCACAATTTATGGGGTACTTAGAGCGTTTCTAGCAGCCTGAGCAACATCCTGTAAGATAACTACCACGTTCAGACCTATAATTCTTTCTACTGGCTCAATTCCAGGAAATGGAATTTCTGCATGAAAATGTATTTTTAAGGCAAAGAGCAGTTTTTAAGTAACCATGGCAGCACACTATTCTGAGCTCGCAGAAGTATAGCGTCACTTGGATGTTAGAATATCCTAGGGGAAAAATGTCATCACTTCTGTCCTTGTTAGCGCGCCAGGAGGGTGAGCTCTCAGGAGGACATCATTCTGGACGCTAACTGGAACCCGATGGCAAGGGAAGCCGGGTGCCAACACTGTCCCTTTGAAGGTTTCAGCCACTCTATAAGCAACAGCATTATCTACATCTTATGGATGATGTAACTGAACCACAAGGCACTTATGTAATTTGTCTAGTCACACAGCTGGGGCAGAATACAAACCTAGGTGGTCAGGCTCCAGCATGATGTACTGGATGGCTGGCAACATCAGCACCATAGTGGCTACCTGTGGGGCTGTCCACTGCATTACAGGCATTGTACTCCTCGTGCTTTGCCTATTTCTCATATGCAAATGGATTATCTTTACAATAACTTTGTGGGGTGAGGAAACCTCAAATGTCTTTGTATTTTTTTTTTCCTAGCCTCCTAGCTTGTCCAGAATCCACCATGCCATCCCTGGGTTCATCCTGCTCTGTAAACGGAAATCTGAGGAGGATGATTAGGGGACCCAGACCCAGATAGCCTCTTCCTCTTCCCTTTGGAAAAAAAAAATCAGACCCAATGAGCATACAACTTCATTTCGTCCGCTGTTTTACATTCTCTAAGTCTGTGTAAATGTCCTCTTCTTGGGACATCTTCCTGGCCACCCTCATTTGAACAATAACCCTTCCAAATAGCCCATCTCCCTTCCAAAGTTTTTCTTTCCTTAGCTTCACAATATTCAGACTCACCATACTTGCAGCCGTCTGTCCCGAGAGTGCTATACCAAATACACACACGCACGCGCGCACACACACACACACACACACACACACACACCACAAAGCCCCCGAGGAAGCACACTTAGTCATTGCTGTGTCTCCTGAGTCTGCAGTAGTGCTGGGCATGTAGAAGATGGTCCATAAATAGTTTGGGTGTTTTGTTTTGCATTTGAGAGGGGGATGACCTCAAATGAATTATGTATTCCAGGCTGACTTCAGACTTACAGTCCTCCTGTCTTAGTTTCCTGAGCACATTGATCACCCGTGTGCAGAGCCATACCCAGCTAGGATACAGTCCTTGAGTGTGTCATTTAACAAACAAACTAAAGACGTGACTAAAAAAAGGGAGTGATAGGAGATGGCCCGGTTGGTAAAATAGTCATCTTGCAAGGACAAGGATATGGGTTCGATCCCCAGAACCCTCATTAAAAACAAAACAAAAACAAAAATCAGGAGAGCCAGGTGTGGTAATACATGGAGTGGAGAGGCAGAGAGAGGCAGATACCTGGGTTGTGGGAGACCGATTGTGCCTAAGGAAAGACTCCTCTGGTCTCTGCACGCATGCGCACACATTCGCACACATTCGCGCACATGCGCACACAGCAGACATAGCAGCACTGCCTTCTGGAAGTTCTTGAGTGAATATGTTTGCCTTTCCTGCTCCTCATTCACCATTTTGACTACAG
Seq C2 exon
GTGTCTGAAAACCTTGTGCAGCGGGATGGGGACTTCCTGGTTCGCGACTCCCTGTCGAGCCCCGGAAACTTTGTCCTGACCTGTCAGTGGAAGAACCTCGCTCAGCACTTTAAGATCAACCGGACTGTCCTGCGGCTCAGCGAGGCCTACAGCCGTGTGCAGTACCAATTCGAGATGGAGAGCTTTGACTCCATCCCGGGGCTGGTCCGCTGCTACGTGGGCAACCGGCGGCCCATCTCCCAACAGAGTGGTGCCATCATCTTCCAGCCCATCAATAGGACAGTGCCCCTCTGGTGTCTGGAGGAGCGTTATGGCACCTCCCCGGGCCGAGGCCGGGAGGGCAGCCTGGCTGAGGGAAGGCCAGACGTGGTGAAGAGGCTGAGCCTCACCACAGGCAGCAGCATCCAGGCTCGGGAACACAGCCTGCCCCGAGGAAACCTCCTCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000028121-Bcar3:NM_013867:4
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact





	

	
ORF disruption upon sequence inclusion





No structure available

		

			
Features


			

				
Disorder rate (Iupred):
  C1=0.116 A=NA C2=0.248
 
                        

				
Domain overlap (PFAM):

					





						

							
C1:
PF0001719=SH2=PU(9.9=18.6)

							
A:
NA

							
C2:
PF0001719=SH2=PD(87.7=47.7)

						

					

				








    
Main Inclusion Isoform:
NA





     
                   









    
Main Skipping Isoform:
ENSMUSP00000029766





     
      









    
Other Inclusion Isoforms:
NA
          









    
Other Skipping Isoforms:
NA
  



Associated events






Conservation


Human
(hg38)
No conservation detected
Human
(hg19)
chr1:94054977-94057821 
Rat
(rn6)
No conservation detected
Cow
(bosTau6)
chr3:50040623-50043601 
LOW PSI
BtaINT0025277
(BCAR3)
Chicken
(galGal4)
chr8:12801887-12803010 
ALTERNATIVE
GgaINT0035716
(BCAR3)
Chicken
(galGal3)
chr8:14552210-14553333 
ALTERNATIVE
GgaINT0035716
(BCAR3)
Zebrafish
(danRer10)
No conservation detected
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"