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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatgtacttcaaagttcaaacatgttatgcttcttattatgtgccttaagaaaaagttcattttattgtttctatatgctccacattaaacagatagctactttggttgaattatcaatgtcaaatccattctttgatcctttaatagtgtcttgctttttagAACAATATTGTTGCCTCTGGTGGCCTTGGTGGGGAGGTTTTTATATGGGATATCGAGGCTGCCCTCGCTCCAGTCTCTAAGTGTAATGATGATACAGTTG

Basic information

species Glycine max
transcript GLYMA03G40440.4
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA03G40440.4 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os12g06810.2 (Oryza sativa), 3'ss of exon 5
gtaatgtacttcaaagttcaaacatgttatgcttcttattatgtgccttaagaaaaagttcattttattgtttctatatgctccacattaaacagatagctactttggttgaattatcaatgtcaaatccattctttgat---cctttaatagtgtcttgctttttagAACAATATTGTTGCCTCTGGTGGCCTTGGTGGGGAGGTTTTTATATGGGATATCGAGGCTGCCCTCGCTCCAGTCTCTAAGTGTAATGATGATACAGTTG
                                                                            |||  |    ||  | ||    |||  | || | ||| ||   || | |   |  || ||| |      |||  |  |    |||  | |||| ||||||||||||||||||||||||||| || ||||| |||||||||||  | ||  || | || ||||| ||  | || | |   ||||  | ||  |
---------------------------------------------------------------------------gtatatt----atccagcactatgcttttctg-tggaactactcattttatcccttttgttttacatgtttttttttattctctgcaatgtagAGCAATATTGTTGCCTCTGGTGGCCTTGGCGGTGAGGTCTTTATATGGGACCTTGATTCTTCTCTTGCTCCTGTGGCCAAATCTGTAGATGCAAAAGAGG

upper sequence: GLYMA03G40440.4 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G167999_T01 (Zea mays), 3'ss of exon 5
gtaatgtacttcaaagttcaaacatgttatgcttcttattatgtgccttaagaaaaagttcattttattgtttctatatgctccacattaaacagatagctactttggttgaattatcaatgtcaaatccattctttgatcctttaatagtgtcttgctttttagAACAATATTGTTGCCTCTGGTGGCCTTGGTGGGGAGGTTTTTATATGGGATATCGAGGCTGCCCTCGCTCCAGTCTCTAAGTGTAATGATGATACAGTTG
                                                                                    | ||||  || |    | ||||   ||   |||   |  |   | |||| |||     |||  |      |||  || |||| ||||||||| ||||||||||| |||||||| |||||||| || |||||  | || ||||| || ||||| ||  | || | |   ||||  | ||  |
---------------------------------------------------------------------------------gtaatattatccacacttgtgctttt-ctgtggtatttttagccttttcattttttacagtttttttgcc--tttgaattgtagAGCAATATTGTAGCCTCTGGTGGTCTTGGTGGTGAGGTTTTCATTTGGGACCTTGATGCTGCTCTTGCTCCTGTAGCCAAATCTGTGGATGCAAAAGAGG

upper sequence: GLYMA03G40440.4 (Glycine max), 3'ss of exon 5
lower sequence: AT3G05090.1 (Arabidopsis thaliana), 3'ss of exon 5
gtaatgtacttcaaagttcaaacatgttatgcttcttattatgtgccttaagaaaaagttcattttattgtttctatatgctccacattaaacagatagctactttggttgaattatcaatgtcaaatccattctttgatcctttaatagtgtcttgctttttagAACAATATTGTTGCCTCTGGTGGCCTTGGTGGGGAGGTTTTTATATGGGATATCGAGGCTGCCCTCGCTCCAGTCTCTAAGTGTAATGATGATACAGTTG
     ||| ||     ||    |||| | |  |  ||||  | | ||     ||||| || |||    || |  |  | | |     || |  | |||  | |||           ||| ||||  || |      |||| || |  |  | ||     |||||||| ||| ||||||| |||||||||||||||||||||||||||||||||||||| || |||||  |  | |||||  | ||   |||||| | ||  |  |
-----gtaatttctcatttgt-catgcttttttctttatagt-tcccactgaaaaaaattgattggtatggtggtgcaagtt-----ttgaggatatatgtgcttc----------tcattgtcgcattc------tgattctatcttgatttcacaacttttagAATAATGTTGTTGCATCTGGTGGCCTTGGTGGGGAGGTTTTTATATGGGATATTGAAGCTGCTTTGTCACCAGTTACCAAACCTAATGACGCTAATGAAG

upper sequence: GLYMA03G40440.4 (Glycine max), 3'ss of exon 5
lower sequence: Vv14s0030g01350.t01 (Vitis vinifera), 3'ss of exon 5
gtaatgtacttcaaagttcaaacatgttatgcttcttattatgtgccttaagaaaaagttcattttattgt-------ttctatatgctccacattaaacagatagctac---tttggttgaattat------caatgtcaaatccattctttgatcctttaatagtgtcttgctttttagAACAATATTGTTGCCTCTGGTGGCCTTGGTGGGGAGGTTTTTATATGGGATATCGAGGCTGCCCTCGCTCCAGTCTCTAAGTGTAATGATGATACAGTTG
     ||| ||      |||||  | | |||    |||||   ||| |  |  ||  |||| | | | |||       || | || | | ||  || ||   |  | | |   |||||  | ||| |         ||||     |||| | ||||||||| |||||||| ||| ||||||| |||| ||||||||||||||||||||||||||||||||||| |||||||| | || ||||| ||  |||||||||| ||||  | |||||  |  |  |
-----gtaatttctttgtcaaaattttcatggaa-ttatttactgcatagatgaagggttcttgtcagtgtaatgctgttatttaagtttcatgttcaatttaatggtgcatatttgggggcattgtgtcatattttgtcgttatcattttctgatccttttatagtgtcatgcattttagAGCAATGTTGTTGCCTCTGGTGGCCTTGGTGGGGAGGTTTTTGTATGGGATCTGGAAGCTGCACTAACTCCAGTCTCAAAGTCAAGTGATGCAATGGAGG

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|209712994|gb|BW684288.1|BW684288
EST:     TCCGGCAACACTCTGACTATGTTACTTGCCTCGCAGCAGCAGNNNNNNNT                         AACAATATTGTTGCCTCTGGTGGCCTTGGTGGGGAGGTTTTTATATGGG
genomic: TCCGGCAACACTCTGACTATGTTACTTGCCTCGCAGCAGCAGAAAAAAATgtaatgtact ... tgctttttagAACAATATTGTTGCCTCTGGTGGCCTTGGTGGGGAGGTTTTTATATGGG






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaattatcaatgtcaaatccattctttgatcctttaatagtgtcttgctttttagAACAATATTGTTGCCTCTGGTGGCCTTGGTGGGGAGGTTTTTATATGGGATATCGAGGCTGCCCTCGCTCCAGTCTCTAAGTGTAATGATGATACAGTTG
                               ctttaat  putative branch site (score: 4)
                                          tcttgcttttt  putative PPT
                                tttaatagt  TA-rich tract