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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgacgccgtttccgccagatttctatttccacttccgttagggtttcctttccaattatttatgatatttttaataatatgatgattttagGTTCAATTAGTTCGAATACAATGGAGAGTGCCGGAGTATGGTTGGACCACGCAGAAGGTCTTTCACTTTCTCAATTTCATTGTGAATGGGG

Basic information

species Glycine max
transcript GLYMA08G09640.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G09640.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G426306_T01 (Zea mays), 3'ss of exon 2
------gtacgacgccgtttccgccagatttctatttccacttccgttagggtttcctttccaattatttatgatatttttaataat--atgatgattttagGTTCAATTAGTTCGAATACAATGGAGAGTGCCGGAGTATGGTTGGACCACGCAGAAGGTCTTTCACTTTCTCAATTTCATTGTGAATGGGG
      ||  ||    ||   |    |      |||   |    ||  |  ||  | |   |    | || ||| |||  |  |  |  ||    ||| |||||  ||||| |  ||||  | || || ||||| |||||||| ||||| ||||||||||| || || ||||| || ||| |||||||||| |
gtgctggtttgat-ttgtggtcttgtgggacgaattgagagaggcggcactgtaacgtccgccgagaattctga-attcgtggtgtttaatttctattgtagGTCAAATTAATCAGAATCGAGTGCAGGGTGCCAGAGTATGGATGGACAACGCAGAAGGTGTTCCATTTTCTAAACTTCCTTGTGAATGGCG

upper sequence: GLYMA08G09640.1 (Glycine max), 3'ss of exon 1
lower sequence: AT1G14530.1 (Arabidopsis thaliana), 3'ss of exon 1
---------------------------------------------------------------------------------------gtacgacgccgtttccgccagatttctatttccacttccg-ttagggtttcctttccaattatttatgatatttttaataatatgatgattttagGTTCAATTAGTTCGAATACAATGGAGAGTGCCGGAGTATGGTTGGACCACGCAGAAGGTCTTTCACTTTCTCAATTTCATTGTGAATGGGG
                                                                                        || ||    |           ||  | | |  | |   | |||| |        || |  ||| || | | ||| | |  | |  |   | ||| ||||||| ||  ||||||||| |||||| || || ||||| ||||| ||||||||||||||||| |||||||||||||| || || || |
gtaccgtttacttgtccttctggttttgaattgggattggaattagggaatgtgttgatttggaatcggaagattaggcatttaaggatatgaaattgaggaaat--agttgttgtatggagtgttgattagagaaaaaaaccctaa-attgattaaagtttcatttgtttttt---tgtagATTCAATTGGTAAGAATACAATTGAGAGTTCCAGAATATGGCTGGACGACGCAGAAGGTCTTTCATTTTCTCAATTTCATGGTTAACGGAG

upper sequence: GLYMA08G09640.1 (Glycine max), 3'ss of exon 1
lower sequence: AT2G02180.1 (Arabidopsis thaliana), 3'ss of exon 1
gtacgacgccgtttccgccagatttctatttccacttccgttagggtttcctttcc-aattatttatgatatttttaataatatgatgattttagGTTCAATTAGTTCGAATACAATGGAGAGTGCCGGAGTATGGTTGGACCACGCAGAAGGTCTTTCACTTTCTCAATTTCATTGTGAATGGGG
                   |  ||||  ||     ||   ||   | ||| |     || |   | | | || ||   |   ||  || ||| || ||||| | ||  ||||||||| |||||| || || ||||||||||| ||||| |||||||||||||||||||||||| |||| ||||| |
-----------------gtacgtttcgtttctggatttgattgatgattcttcgatgaaattggtgtaacatcttatgtttgattttggttt-agATTCAACTTGTGAGAATACAATTGAGAGTTCCTGAATATGGTTGGACGACGCAAAAGGTCTTTCACTTTCTCAATTTCGTTGTTAATGGAG

upper sequence: GLYMA08G09640.1 (Glycine max), 3'ss of exon 1
lower sequence: EFJ23006 (Selaginella moellendorffii), 3'ss of exon 1
gtacgacgccgtttccgccagatttctatttccacttccgttagggtttcctttccaattatttatgat-atttttaataatatgatgattttagGTTCAATTAGTTCGAATACAATGGAGAGTGCCGGAGTATGGTTGGACCACGCAGAAGGTCTTTCACTTTCTCAATTTCATTGTGAATGGGG
                      | |  | | | |||    ||  ||  || |||| | | |||  ||   | |  |    || |     |   || | ||| |  | || ||  |     | || || |||||||| |||||||||||||||||||| || || || |||||| |||| ||||| |
---------------------gtatggaatccgactagttttctgg--tcttttctattgattcttggggaatcgtggcgatttctc--tcgcagATACAACTCATCCGGATCGAGATTCGCGTCCCCGAGTATGGCTGGACCACGCAGAAGGTCTTCCATTTGCTGAATTTCCTTGTAAATGGAG

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|213611111|gb|DB972699.1|DB972699
EST:     TCTTCCACCTCCTCTCCATCCTCTACGGAATCGTCGCCGCCGTCGCTCTA                         GTTCAATTAGTTCGAATACAATGGAGAGTGCCGGAGTATGGTTGGACCACG
genomic: TCTTCCACCTCCTCTCCATCCTCTACGGAATCGTCGCCGCCGTCGCTCTAgtacgacgcc ... atgattttagGTTCAATTAGTTCGAATACAATGGAGAGTGCCGGAGTATGGTTGGACCACG
EST: gi|193613466|gb|FK565092.1|FK565092
EST:     TCTTCCACCTCCTCTCCATCCTCTACGGAATCGTCGCCGCCGTCGCTCTA                         GTTCAATTAGTTCGAATACAATGGAGAGTGCCGGAGTATGGTTGGACCACG
genomic: TCTTCCACCTCCTCTCCATCCTCTACGGAATCGTCGCCGCCGTCGCTCTAgtacgacgcc ... atgattttagGTTCAATTAGTTCGAATACAATGGAGAGTGCCGGAGTATGGTTGGACCACG
EST: gi|208092250|gb|GD888909.1|GD888909
EST:     TCTTCCACCTCCTCTCCATCCTCTACGGAATCGTCGCCGCCGTCGCTCTA                         GTTCAATTAGTTCGAATACAATGGAGAGTGCCGGAGTATGGTTGGACCACG
genomic: TCTTCCACCTCCTCTCCATCCTCTACGGAATCGTCGCCGCCGTCGCTCTAgtacgacgcc ... atgattttagGTTCAATTAGTTCGAATACAATGGAGAGTGCCGGAGTATGGTTGGACCACG
EST: gi|192314057|gb|FK008797.1|FK008797
EST:     TCTTCCACCTCCTCTCCATCCTCTACGGAATCGTCGCCGCCGTCGCTCTA                         GTTCAATTAGTTCGAATACAATGGAGAGTGCCGGAGTATGGTTGGACCACA
genomic: TCTTCCACCTCCTCTCCATCCTCTACGGAATCGTCGCCGCCGTCGCTCTAgtacgacgcc ... atgattttagGTTCAATTAGTTCGAATACAATGGAGAGTGCCGGAGTATGGTTGGACCACG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttagggtttcctttccaattatttatgatatttttaataatatgatgattttagGTTCAATTAGTTCGAATACAATGGAGAGTGCCGGAGTATGGTTGGACCACGCAGAAGGTCTTTCACTTTCTCAATTTCATTGTGAATGGGG
                                ttttaat  putative branch site (score: 3)
                 aattatttatgatatt  TA-rich tract