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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgttcttttggcttcttgacatatatataactgctactactttttatttttaatcaatatcttcttgtttaagaactcgaacaatccctgtttggtttagGGTGGTAAATGGTGCCCTTGAATACCTTGCTAAGGATCTTGGAATCACTGAAAATACTGTTATACAAG

Basic information

species Glycine max
transcript GLYMA13G07780.2
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA13G07780.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G098011_T02 (Zea mays), 3'ss of exon 3
----------------------------------------------------------------------------------tgttcttttggcttcttgacatatatataactgctactactttttattt--ttaatcaatatcttc-ttgtttaagaactcgaacaatccctgtt-tgg--tttagGGTGGTAAATGGTGCCCTTGAATACCTTGCTAAGGATCTTGGAATCACTGAAAATACTGTTATACAAG
                                                                                          |  |    ||| |   | |||  | |  ||  | |  | ||   |  | || |       ||||  | ||  | |  ||||| | |  |||  | ||| ||||| |||||||| |||||||| ||||| ||||||||||||||  |||||||| | ||  ||||  
gtatgtactttatcactactacaagatgattgtttcttaaacacaattggataaagcataatttactgcattttaattgatgaaaatgaataacaagctgaaaataaaatagttccatcttttctgcacttatcttgtgaacacaaaaactgttagataataccaggaatccatttcatggaatgtagTGTGGTCAATGGTGCGCTTGAATATCTTGCGAAGGATCTTGGAATTGCTGAAAATGCCGTCTTACAG-

upper sequence: GLYMA13G07780.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G098011_T01 (Zea mays), 3'ss of exon 3
----------------------------------------------------------------------------------tgttcttttggcttcttgacatatatataactgctactactttttatt--tttaatcaatatcttc-ttgtttaagaactcgaacaatccctgtt-tgg--tttagGGTGGTAAATGGTGCCCTTGAATACCTTGCTAAGGATCTTGGAATCACTGAAAATACTGTTATACAAG
                                                                                          |  |    ||| |   | |||  | |  ||  | |  | |  | |  | || |       ||||  | ||  | |  ||||| | |  |||  | ||| ||||| |||||||| |||||||| ||||| ||||||||||||||  |||||||| | ||  |||| |
gtatgtactttatcactactacaagatgattgtttcttaaacacaattggataaagcataatttactgcattttaattgatgaaaatgaataacaagctgaaaataaaatagttccatcttttctgcacttatcttgtgaacacaaaaactgttagataataccaggaatccatttcatggaatgtagTGTGGTCAATGGTGCGCTTGAATATCTTGCGAAGGATCTTGGAATTGCTGAAAATGCCGTCTTACAGG

upper sequence: GLYMA13G07780.1 (Glycine max), 3'ss of exon 3
lower sequence: AT5G16150.1 (Arabidopsis thaliana), 3'ss of exon 3
tgttcttttggcttcttgacatatatataactgctactactttttatttttaatcaatatcttcttgtttaagaactcgaacaatccctgtttggtttagGGTGGTAAATGGTGCCCTTGAATACCTTGCTAAGGATCTTGGAATCACTGAAAATACTGTTATACAAG
                     |||   ||| | |||| ||| ||| | | |      | |  || ||  | |  |         |    |  ||  | |||||||| |||||||| |||||||| ||||||||||||||||| ||| | |||||||||||| | ||||
--------------------gtatgactaaatactac-actgtttttatct---tggtgtgatcatggatgatgat----gttctattggactgaatcagGGTGGTTAATGGTGCTCTTGAATATCTTGCTAAGGATCTTGGGATCGCCGAAAATACTGTTTTGCAAG

upper sequence: GLYMA13G07780.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv14s0006g02720.t01 (Vitis vinifera), 3'ss of exon 3
--tgttcttttggcttcttgacatatatataactgctactactttttatttttaatcaatatcttcttgtttaagaactcgaacaatccctgtttggtttagGGTGGTAAATGGTGCCCTTGAATACCTTGCTAAGGATCTTGGAATCACTGAAAATACTGTTATACAAG
  |    ||  | ||| |||      | |      |   ||    |||| | |    || || | || ||   ||     |   | |   | ||||    |||||||| |||||||| |||||||||||| | ||||||||||||||  |||||||| ||||| ||||||
aatacagttaagtctttttgtatgcaacagggtctcatgtataacttatctatgggtaagatgtact-gtaacagtgtatgc-tattttttatttgccacagGGTGGTGAATGGTGCTCTTGAATACCTTTCCAAGGATCTTGGAATTGCTGAAAATGCTGTTTTACAAG

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|213605474|gb|DB964613.1|DB964613
EST:     TATGTTGGTGTTGCTTGCCTCGGAGCCATTTTATTTGGTTATCATCTCGG                         GGTGGTAAATGGTGCCCTTGAATACCTTGCTAAGGATCTTGGAATCACTGA
genomic: TATGTTGGTGTTGCTTGCCTCGGAGCCATTTTATTTGGTTATCATCTCGGgtatggatag ... tttggtttagGGTGGTAAATGGTGCCCTTGAATACCTTGCTAAGGATCTTGGAATCACTGA
EST: gi|209725014|gb|BW663004.1|BW663004
EST:     TATGTTGGTGTTGCTTGCCTCGGAGCCATTTTATTTGGTTATCATCTCGG                         GGTGGTAAATGGTGCCCTTGAATACCTTGCTAAGAATCTTGGAATCACTGA
genomic: TATGTTGGTGTTGCTTGCCTCGGAGCCATTTTATTTGGTTATCATCTCGGgtatggatag ... tttggtttagGGTGGTAAATGGTGCCCTTGAATACCTTGCTAAGGATCTTGGAATCACTGA
EST: gi|213608297|gb|DB972639.1|DB972639
EST:     TATGTTGGTGTTGCTTGCCTCGGAGCCATTTTATTTGGTTATCATCTCGG                         GGTGGTAAATGGTGCCCTTGAATACCTTGCTAAGGATCTTGGAATCACTGA
genomic: TATGTTGGTGTTGCTTGCCTCGGAGCCATTTTATTTGGTTATCATCTCGGgtatggatag ... tttggtttagGGTGGTAAATGGTGCCCTTGAATACCTTGCTAAGGATCTTGGAATCACTGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atttttaatcaatatcttcttgtttaagaactcgaacaatccctgtttggtttagGGTGGTAAATGGTGCCCTTGAATACCTTGCTAAGGATCTTGGAATCACTGAAAATACTGTTATACAAG
  ttttaat  putative branch site (score: 3)
                                       tccctgttt  putative PPT
     taatcaatat  TA-rich tract