Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   		9  
 5'  3'   		10  
 5'  3'   		11  
 5'  3'   		12  
 5'  3'   		13  
 5'  3'   		14  
 5'  3'   		15  
 5'  3'   		16  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattgcactcttcacgtaacataataagaatgacattttgtgatgattacaagactagtcaacagccagtttcagtacacattttcccctaaagaccttttttgctttatttgaagGTTGTCCGAGTGTGGGATCCGAGGACAGGATCGAAAAACATGAAATTGAGAGGGCACACTGACAATATCAGAGCCTTGCTTGTTGATTCTACAGGGAG

Basic information

species Zea mays
transcript GRMZM2G167999_T02
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G167999_T02 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os12g06810.2 (Oryza sativa), 3'ss of exon 6
gtattgcactcttcacgtaacataataagaatg-acattttgtgatgattacaagactagtcaaca-gccagtttcagtacacattttcccctaaagaccttttttgctttattt---------------------gaagGTTGTCCGAGTGTGGGATCCGAGGACAGGATCGAAAAACATGAAATTGAGAGGGCACACTGACAATATCAGAGCCTTGCTTGTTGATTCTACAGGGAG
|||||    ||||||  |   | ||| || ||| |  |||  |   | |||  || |     ||   || | ||||  |  ||   ||     | |||||| |  ||   |||||                     | ||||||| || || |||||||| ||||| || || || || |||||||||||||||||||||||||||||||| || || ||| ||||| |||| || ||
gtattatgttcttcatctttgagaatgagtatgcaagtttccttggggttaggaggcaccataatgtgcgaatttctttggactgcttttg--agagacctctcctgtgatatttccttatatgtacctgtttagtgtagGTTGTTCGCGTTTGGGATCCCAGGACTGGTTCAAAGAAAATGAAATTGAGAGGGCACACTGACAATATCAGGGCTTTACTTCTTGATCCTACTGGCAG
















Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|71433407|gb|DR814457.1|DR814457
EST:     TGGCGATGAATGATACAGGAACCCTTCTTCTCTCTGGTGGCACTGAGAAG                         GTTGTCCGAGTGTGGGATCCGAGGACAGGATCGAAAAACATGAAATTGAGA
genomic: TGGCGATGAATGATACAGGAACCCTTCTTCTCTCTGGTGGCACTGAGAAGgtattgcact ... ttatttgaagGTTGTCCGAGTGTGGGATCCGAGGACAGGATCGAAAAACATGAAATTGAGA
EST: gi|18385199|gb|BM418398.1|BM418398
EST:     TGGCGATGAATGATACAGGAACCCTTCTTCTCTCTGGTGGCACTGAGAAG                         GTTGTCCGAGTGTGGGATCCGAGGACAGGATCGAAAAACATGAAATTGAGA
genomic: TGGCGATGAATGATACAGGAACCCTTCTTCTCTCTGGTGGCACTGAGAAGgtattgcact ... ttatttgaagGTTGTCCGAGTGTGGGATCCGAGGACAGGATCGAAAAACATGAAATTGAGA

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 4 RNA-Seq libraries.


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 142

TGGGTACAGTCCAATAGCTGCCAAAGGTCACAAAGATTCAGTTTACGCACTGGCGATGAATGATACAGGAACCCTTCTTCTCTCTGGTGGCACTGAGAAGgtattgcact ... ttatttgaagGTTGTCCGAGTGTGGGATCCGAGGACAGGATCGAAAAACATGAAATTGAGAGGGCACACTGACAATATCAGAGCCTTGCTTGTTGATTCTACAGGGAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 181

TGGGTACAGTCCAATAGCTGCCAAAGGTCACAAAGATTCAGTTTACGCACTGGCGATGAATGATACAGGAACCCTTCTTCTCTCTGGTGGCACTGAGAAGgtattgcact ... ttatttgaagGTTGTCCGAGTGTGGGATCCGAGGACAGGATCGAAAAACATGAAATTGAGAGGGCACACTGACAATATCAGAGCCTTGCTTGTTGATTCTACAGGGAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 147

TGGGTACAGTCCAATAGCTGCCAAAGGTCACAAAGATTCAGTTTACGCACTGGCGATGAATGATACAGGAACCCTTCTTCTCTCTGGTGGCACTGAGAAGgtattgcact ... ttatttgaagGTTGTCCGAGTGTGGGATCCGAGGACAGGATCGAAAAACATGAAATTGAGAGGGCACACTGACAATATCAGAGCCTTGCTTGTTGATTCTACAGGGAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 178

TGGGTACAGTCCAATAGCTGCCAAAGGTCACAAAGATTCAGTTTACGCACTGGCGATGAATGATACAGGAACCCTTCTTCTCTCTGGTGGCACTGAGAAGgtattgcact ... ttatttgaagGTTGTCCGAGTGTGGGATCCGAGGACAGGATCGAAAAACATGAAATTGAGAGGGCACACTGACAATATCAGAGCCTTGCTTGTTGATTCTACAGGGAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acagccagtttcagtacacattttcccctaaagaccttttttgctttatttgaagGTTGTCCGAGTGTGGGATCCGAGGACAGGATCGAAAAACATGAAATTGAGAGGGCACACTGACAATATCAGAGCCTTGCTTGTTGATTCTACAGGGAG
                         ccctaaa  putative branch site (score: 178)
                                  ccttttttgctttatt  putative PPT
                                    ttttttgctttattt  TA-rich tract