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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgaagttttacatgttggatatccattctcttgttgataagccatcctccacttgttcatttattttttcagtacatatttttcagGTAAAGAGTGTTTTTGGTGCAAAAATGTTTGCACTTGGGGTTGTAGTCAAGATTCCTGTTCCAAAACAAACAGCAAAAACAAATTTCACAGTTACATCTG

Basic information

species Glycine max
transcript GLYMA05G23670.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA05G23670.2 (Glycine max), 3'ss of exon 9
lower sequence: AT5G46630.1 (Arabidopsis thaliana), 3'ss of exon 9
gtttgaagttttacatgttggatatccattctcttgttgataagccatcctccacttgttcatttattttttcagtacatatttt--tcagGTAAAGAGTGTTTTTGGTGCAAAAATGTTTGCACTTGGGGTTGTAGTCAAGATTCCTGTTCCAAAACAAACAGCAAAAACAAATTTCACAGTTACATCTG
||    |  ||| |     |  ||     |          |        ||   ||   | |       || | ||   |  | |  |||||| || ||||| |||||||| ||||||||||| |||||||| || || || ||||| || |||||||||||||| || || ||||||  ||| ||| |||
gtacataacttttctcaaggattacaggatacaaaaaaattggcttgatctttgctctcttacaatcccttcccgtgttttgtctgttcagGTCAAAAGTGTGTTTGGTGCTAAAATGTTTGCCCTTGGGGTCGTGGTTAAAATTCCAGTGCCAAAACAAACAGCCAAGACCAATTTCCAAGTGACAACTG

upper sequence: GLYMA05G23670.2 (Glycine max), 3'ss of exon 9
lower sequence: PP1S54_156V6.1 (Physcomitrella patens), 3'ss of exon 9
------------------------------------------------------------------------------gtttgaagttttacatgttggatatccat--tctcttgttgataagccatcctccacttgttcatttattttttcagtacatatttttcagGTAAAGAGTGTTTTTGGTGCAAAAATGTTTGCACTTGGGGTTGTAGTCAAGATTCCTGTTCCAAAACAAACAGCAAAAACAAATTTCACAGTTACATCTG
                                                                              | |  | |  |   || | | || |  |   |  |||||||||  | ||     ||| |   ||    | ||  |  |||      ||||||| |||||||| ||||| || ||||||||||||||||| || || |||||| | |||||||| || || ||||| ||  | |||||    || || ||||
gtgagatggatagccctcacgctgcgacgaacagtactctgttgatagtgtgtcttaaattcagtaacattagttccagatgcatggctacgatatagaatgtttagaatgccttgttgatgcgtcaa----cacgtcgccaacagtgtt--cgatactgcacgttcagGTCAAGAGTGTATTTGGGGCCAAAATGTTTGCACTTGGAGTGGTGGTCAAGGTGCCTGTTCCCAAGCACACAGCCAAGGCTAATTTTCAGGTGACCTCTG
















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|51335623|gb|CO979489.1|CO979489
EST:     TGCCAACCATCAAGGAACTTGGTCGATCACGGATAGAAGTGAACGTTAAG                         GTAAAGAGTGTTTTTGGTGCAAAAATGTTTGCACTTGGGGTTGTAGTCAAG
genomic: TGCCAACCATCAAGGAACTTGGTCGATCACGGATAGAAGTGAACGTTAAGgtttgaagtt ... tatttttcagGTAAAGAGTGTTTTTGGTGCAAAAATGTTTGCACTTGGGGTTGTAGTCAAG
EST: gi|254344956|gb|GR851439.1|GR851439
EST:     CAACCATCAAGGAACTTGGTCGATCACGGATAGAAGTGAACGTTAAG                         GTAAAGAGTGTTTTTGGTGCAAAAATGTTTGCACTTGGGGTTGTAGTCAAG
genomic: CAACCATCAAGGAACTTGGTCGATCACGGATAGAAGTGAACGTTAAGgtttgaagtt ... tatttttcagGTAAAGAGTGTTTTTGGTGCAAAAATGTTTGCACTTGGGGTTGTAGTCAAG
EST: gi|58020847|gb|CX707589.1|CX707589
EST:     TGCCAACCATCAAGGAACTTGGTCGATCACGGATAGAAGTGAACGTTAAG                         GTAAAGAGTGTTTTTGGTGCAAAAATGTTTGCACTTGGGGTTGTAGTCAAG
genomic: TGCCAACCATCAAGGAACTTGGTCGATCACGGATAGAAGTGAACGTTAAGgtttgaagtt ... tatttttcagGTAAAGAGTGTTTTTGGTGCAAAAATGTTTGCACTTGGGGTTGTAGTCAAG
EST: gi|254344955|gb|GR851438.1|GR851438
EST:     CAACCATCAAGGAACTTGGTCGATCACGGATAGAAGTGAACGTTAAG                         GTAAAGAGTGTTTTTGGTGCAAAAATGTTTGCACTTGGGGTTGTAGTCAAG
genomic: CAACCATCAAGGAACTTGGTCGATCACGGATAGAAGTGAACGTTAAGgtttgaagtt ... tatttttcagGTAAAGAGTGTTTTTGGTGCAAAAATGTTTGCACTTGGGGTTGTAGTCAAG
EST: gi|208054657|gb|GD855732.1|GD855732
EST:     TGCCAACCATCAAGGAACTTGGTCGATCACGGATAGAAGTGAACGTTAAG                         GTAAAGAGTGTTTTTGGTGCAAAAATGTTTGCACTTGGGGTTGTAGTCAAG
genomic: TGCCAACCATCAAGGAACTTGGTCGATCACGGATAGAAGTGAACGTTAAGgtttgaagtt ... tatttttcagGTAAAGAGTGTTTTTGGTGCAAAAATGTTTGCACTTGGGGTTGTAGTCAAG
EST: gi|58017189|gb|CX703931.1|CX703931
EST:     TGCCAACCATCAAGGAACTTGGTCGATCACGGATAGAAGTGAACGTTAAG                         GTAAAGAGTGTTTTTGGTGCAAAAATGTTTGCACTTGGGGTTGTAGTCAAG
genomic: TGCCAACCATCAAGGAACTTGGTCGATCACGGATAGAAGTGAACGTTAAGgtttgaagtt ... tatttttcagGTAAAGAGTGTTTTTGGTGCAAAAATGTTTGCACTTGGGGTTGTAGTCAAG
EST: gi|58017359|gb|CX704101.1|CX704101
EST:     GCCCAACCATCAAGGAACTTGGTCGATCACGGATAGAAGTGAACGTTAAG                         GTAAAGAGTGTTTTTGGTGCAAAAATGTTTGCACTTGGGGTTGTAGTCAAG
genomic: G-CCAACCATCAAGGAACTTGGTCGATCACGGATAGAAGTGAACGTTAAGgtttgaagtt ... tatttttcagGTAAAGAGTGTTTTTGGTGCAAAAATGTTTGCACTTGGGGTTGTAGTCAAG
EST: gi|16349156|gb|BI974751.1|BI974751
EST:     TGCCAACCATCAAGGAACTTGGTCGATCACGGATAGAAGTGAACGTTAAG                         GTAAAGAGTGTTTTTGGTGCAAAAATGTTTGCACTTGGGGTTGTAGTCAAG
genomic: TGCCAACCATCAAGGAACTTGGTCGATCACGGATAGAAGTGAACGTTAAGgtttgaagtt ... tatttttcagGTAAAGAGTGTTTTTGGTGCAAAAATGTTTGCACTTGGGGTTGTAGTCAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgttgataagccatcctccacttgttcatttattttttcagtacatatttttcagGTAAAGAGTGTTTTTGGTGCAAAAATGTTTGCACTTGGGGTTGTAGTCAAGATTCCTGTTCCAAAACAAACAGCAAAAACAAATTTCACAGTTACATCTG
 tgttgat  putative branch site (score: 4)
                                             tatttttc  putative PPT
                        ttcatttattttttca  TA-rich tract